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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. | 198 | <span·class="go">array([[0.11889108,·0.99563736,·0.4708511·],</span> |
| 199 | <span·class="go">·······[0.11030402,·0.22456077,·0.749747··],</span> | ||
| 200 | <span·class="go">·······[0.9887107·,·0.75898975,·0.7610922·],</span> | ||
| 201 | <span·class="go">·······[0.03039484,·0.1537153·,·0.0294544·],</span> | ||
| 199 | <span·class="go">·······[0. | 202 | <span·class="go">·······[0.03143189,·0.5109341·,·0.8765838·],</span> |
| 200 | <span·class="go">·······[0.30248833,·0.5658569·,·0.5956299·],</span> | ||
| 201 | <span·class="go">·······[0.07117487,·0.49016574,·0.64954334],</span> | ||
| 202 | <span·class="go">·······[0.69 | 203 | <span·class="go">·······[0.46935037,·0.02496142,·0.44709668],</span> |
| 203 | <span·class="go">·······[0.5 | 204 | <span·class="go">·······[0.5878508·,·0.15341844,·0.24387108],</span> |
| 204 | <span·class="go">·······[0.0047781·,·0.1330923·,·0.3930967·],</span> | ||
| 205 | <span·class="go">·······[0. | 205 | <span·class="go">·······[0.8923092·,·0.50627977,·0.9575663·],</span> |
| 206 | <span·class="go">·······[0. | 206 | <span·class="go">·······[0.19825953,·0.4598811·,·0.98291963]],·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([[0.09652414,·0.61696154,·0.03166472],</span> | ||
| 241 | <span·class="go">array([[0.41265997,·0.51989734,·0.5874644·],</span> | ||
| 242 | <span·class="go">·······[0.63586783,·0.09243915,·0.8981873·],</span> | ||
| 243 | <span·class="go">·······[0.3 | 242 | <span·class="go">·······[0.3301086·,·0.83354086,·0.7155698·],</span> |
| 243 | <span·class="go">·······[0.729872··,·0.9966624·,·0.1752343·],</span> | ||
| 244 | <span·class="go">·······[0.72815806,·0.04989876,·0.24340108],</span> | ||
| 245 | <span·class="go">·······[0.0090039·,·0.24569628,·0.90215504],</span> | ||
| 244 | <span·class="go">·······[0. | 246 | <span·class="go">·······[0.42624676,·0.25213456,·0.12603416],</span> |
| 245 | <span·class="go">·······[0.83061415,·0.9239881·,·0.5580153·],</span> | ||
| 246 | <span·class="go">·······[0.8071852·,·0.29288206,·0.63318837],</span> | ||
| 247 | <span·class="go">·······[0. | 247 | <span·class="go">·······[0.8968407·,·0.24936676,·0.5196016·]],·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([[0.63889754,·0.10892821,·0.00807442], | ||
| 111 | ·······[0.42598215,·0.9713994·,·0.8758309·], | ||
| 112 | ·······[0.30248833,·0.5658569·,·0.5956299·], | ||
| 113 | ·······[0.07117487,·0.49016574,·0.64954334], | ||
| 114 | ·······[0.69813335,·0.6075195·,·0.18205918], | ||
| 115 | ·······[0.5712853·,·0.8626947·,·0.31959438], | ||
| 116 | ·······[0.0047781·,·0.1330923·,·0.3930967·], | ||
| 117 | 110 | array([[0.11889108,·0.99563736,·0.4708511·], | |
| 111 | ·······[0.11030402,·0.22456077,·0.749747··], | ||
| 112 | ·······[0.9887107·,·0.75898975,·0.7610922·], | ||
| 113 | ·······[0.03039484,·0.1537153·,·0.0294544·], | ||
| 114 | ·······[0.03143189,·0.5109341·,·0.8765838·], | ||
| 115 | ·······[0.46935037,·0.02496142,·0.44709668], | ||
| 116 | ·······[0.5878508·,·0.15341844,·0.24387108], | ||
| 117 | ·······[0.8923092·,·0.50627977,·0.9575663·], | ||
| 118 | ·······[0. | 118 | ·······[0.19825953,·0.4598811·,·0.98291963]],·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([[0.41265997,·0.51989734,·0.5874644·], | ||
| 148 | ·······[0.63586783,·0.09243915,·0.8981873·], | ||
| 149 | ·······[0.3649701·,·0.58789736,·0.98103064], | ||
| 150 | ·······[0.6755696·,·0.52513665,·0.43279934], | ||
| 151 | ·······[0.83061415,·0.9239881·,·0.5580153·], | ||
| 152 | ·······[0.8071852·,·0.29288206,·0.63318837], | ||
| 153 | 147 | array([[0.09652414,·0.61696154,·0.03166472], | |
| 148 | ·······[0.3301086·,·0.83354086,·0.7155698·], | ||
| 149 | ·······[0.729872··,·0.9966624·,·0.1752343·], | ||
| 150 | ·······[0.72815806,·0.04989876,·0.24340108], | ||
| 151 | ·······[0.0090039·,·0.24569628,·0.90215504], | ||
| 152 | ·······[0.42624676,·0.25213456,·0.12603416], | ||
| 153 | ·······[0.8968407·,·0.24936676,·0.5196016·]],·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 | ········"11889108":·8, | ||
| 817 | ········"99563736":·8, | ||
| 818 | ········"4708511":·8, | ||
| 819 | ········"11030402":·8, | ||
| 820 | ········"22456077":·8, | ||
| 821 | ········"749747":·8, | ||
| 822 | ········"9887107":·8, | ||
| 816 | ········" | 823 | ········"75898975":·8, |
| 817 | ········"10 | 824 | ········"7610922":·8, |
| 818 | ········"0 | 825 | ········"03039484":·8, |
| 819 | ········"42598215":·8, | ||
| 820 | ········"9713994":·8, | ||
| 821 | ········"8758309":·8, | ||
| 822 | ········"30248833":·8, | ||
| 823 | ········"5658569":·8, | ||
| 824 | ········"5956299":·8, | ||
| 825 | ········"07117487":·8, | ||
| 826 | ········"49016574":·8, | ||
| 827 | ········"64954334":·8, | ||
| 828 | ········"69813335":·8, | ||
| 829 | ········"6075195":·8, | ||
| 830 | ········"18205918":·8, | ||
| 831 | ········"571 | 826 | ········"1537153":·8, |
| 832 | ········" | 827 | ········"0294544":·8, |
| 833 | ········"31 | 828 | ········"03143189":·8, |
| 834 | ········"0047781":·8, | ||
| 835 | ········" | 829 | ········"5109341":·8, |
| 830 | ········"8765838":·8, | ||
| 836 | ········" | 831 | ········"46935037":·8, |
| 837 | ········" | 832 | ········"02496142":·8, |
| 838 | ········" | 833 | ········"44709668":·8, |
| 839 | ········" | 834 | ········"5878508":·8, |
| 835 | ········"15341844":·8, | ||
| 836 | ········"24387108":·8, | ||
| 837 | ········"8923092":·8, | ||
| 838 | ········"50627977":·8, | ||
| 840 | ········" | 839 | ········"9575663":·8, |
| 840 | ········"19825953":·8, | ||
| 841 | ········"4 | 841 | ········"4598811":·8, |
| 842 | ········" | 842 | ········"98291963":·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 | ········"41265997":·8, | ||
| 848 | ········"51989734":·8, | ||
| 849 | ········"5874644":·8, | ||
| 850 | ········"63586783":·8, | ||
| 851 | ········"09 | 847 | ········"09652414":·8, |
| 852 | ········" | 848 | ········"61696154":·8, |
| 853 | ········"36 | 849 | ········"03166472":·8, |
| 854 | ········"58789736":·8, | ||
| 855 | ········" | 850 | ········"3301086":·8, |
| 851 | ········"83354086":·8, | ||
| 856 | ········" | 852 | ········"7155698":·8, |
| 857 | ········"52513665":·8, | ||
| 858 | ········"43279934":·8, | ||
| 859 | ········"83061415":·8, | ||
| 860 | ········" | 853 | ········"729872":·8, |
| 861 | ········" | 854 | ········"9966624":·8, |
| 862 | ········" | 855 | ········"1752343":·8, |
| 863 | ········" | 856 | ········"72815806":·8, |
| 857 | ········"04989876":·8, | ||
| 864 | ········" | 858 | ········"24340108":·8, |
| 859 | ········"0090039":·8, | ||
| 860 | ········"24569628":·8, | ||
| 861 | ········"90215504":·8, | ||
| 865 | ········" | 862 | ········"42624676":·8, |
| 863 | ········"25213456":·8, | ||
| 866 | ········" | 864 | ········"12603416":·8, |
| 867 | ········" | 865 | ········"8968407":·8, |
| 866 | ········"24936676":·8, | ||
| 867 | ········"5196016":·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, |