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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([[0.922 | 198 | <span·class="go">array([[0.19622535,·0.10364336,·0.73504···],</span> |
| 199 | <span·class="go">·······[0. | 199 | <span·class="go">·······[0.42037013,·0.12902392,·0.12509118],</span> |
| 200 | <span·class="go">·······[0.85473853,·0.4855717·,·0.2546638·],</span> | ||
| 200 | <span·class="go">·······[0.4006521·,·0.411183··,·0.3869858·],</span> | ||
| 201 | <span·class="go">·······[0.6653195·,·0.40534142,·0.89931124],</span> | ||
| 202 | <span·class="go">·······[0.09279376,·0.57808363,·0.6925787·],</span> | ||
| 203 | <span·class="go">·······[0. | 201 | <span·class="go">·······[0.03070883,·0.9847538·,·0.9913866·],</span> |
| 202 | <span·class="go">·······[0.36848673,·0.88404053,·0.8322486·],</span> | ||
| 204 | <span·class="go">·······[0. | 203 | <span·class="go">·······[0.26584858,·0.26227···,·0.3523023·],</span> |
| 205 | <span·class="go">·······[0. | 204 | <span·class="go">·······[0.5500672·,·0.7017762·,·0.21717823],</span> |
| 205 | <span·class="go">·······[0.0484382·,·0.25592637,·0.83795255],</span> | ||
| 206 | <span·class="go">·······[0. | 206 | <span·class="go">·······[0.31152233,·0.53387904,·0.95502675]],·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([[2.7918157e-01,·1.8956065e-01,·4.3768886e-01],</span> | ||
| 242 | <span·class="go">·······[7.6041305e-01,·8.9359033e-01,·3.1214675e-01],</span> | ||
| 243 | <span·class="go">·······[4.8658469e-01,·8.3486205e-01,·9.3346763e-01],</span> | ||
| 244 | <span·class="go">·······[9.6316226e-02,·3.5347688e-01,·3.0949745e-01],</span> | ||
| 245 | <span·class="go">·······[7.7243263e-01,·7.8227520e-01,·6.0253316e-01],</span> | ||
| 246 | <span·class="go">·······[8.9934774e-02,·5.6932104e-01,·4.4514567e-01],</span> | ||
| 247 | <span·class="go"> | 241 | <span·class="go">array([[0.23688282,·0.9630058·,·0.6336629·],</span> |
| 242 | <span·class="go">·······[0.07506042,·0.25881794,·0.2790243·],</span> | ||
| 243 | <span·class="go">·······[0.7146926·,·0.37712127,·0.8139112·],</span> | ||
| 244 | <span·class="go">·······[0.76515955,·0.8881079·,·0.290039··],</span> | ||
| 245 | <span·class="go">·······[0.9350002·,·0.7703131·,·0.98512655],</span> | ||
| 246 | <span·class="go">·······[0.52404183,·0.5848071·,·0.93785363],</span> | ||
| 247 | <span·class="go">·······[0.11575463,·0.48285633,·0.03564102]],·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([[0.9223388·,·0.22633724,·0.07840342], | ||
| 111 | ·······[0.6045313·,·0.13220368,·0.44016424], | ||
| 112 | ·······[0.4006521·,·0.411183··,·0.3869858·], | ||
| 113 | ·······[0.6653195·,·0.40534142,·0.89931124], | ||
| 114 | ·······[0.09279376,·0.57808363,·0.6925787·], | ||
| 115 | ·······[0.34779903,·0.69938034,·0.3338973·], | ||
| 116 | ·······[0.11514353,·0.2545868·,·0.20324644], | ||
| 117 | ·······[0.16607866,·0.16386276,·0.9034168·], | ||
| 118 | 110 | array([[0.19622535,·0.10364336,·0.73504···], | |
| 111 | ·······[0.42037013,·0.12902392,·0.12509118], | ||
| 112 | ·······[0.85473853,·0.4855717·,·0.2546638·], | ||
| 113 | ·······[0.03070883,·0.9847538·,·0.9913866·], | ||
| 114 | ·······[0.36848673,·0.88404053,·0.8322486·], | ||
| 115 | ·······[0.26584858,·0.26227···,·0.3523023·], | ||
| 116 | ·······[0.5500672·,·0.7017762·,·0.21717823], | ||
| 117 | ·······[0.0484382·,·0.25592637,·0.83795255], | ||
| 118 | ·······[0.31152233,·0.53387904,·0.95502675]],·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([[2.7918157e-01,·1.8956065e-01,·4.3768886e-01], | ||
| 148 | ·······[7.6041305e-01,·8.9359033e-01,·3.1214675e-01], | ||
| 149 | ·······[4.8658469e-01,·8.3486205e-01,·9.3346763e-01], | ||
| 150 | ·······[9.6316226e-02,·3.5347688e-01,·3.0949745e-01], | ||
| 151 | ·······[7.7243263e-01,·7.8227520e-01,·6.0253316e-01], | ||
| 152 | ·······[8.9934774e-02,·5.6932104e-01,·4.4514567e-01], | ||
| 153 | 147 | array([[0.23688282,·0.9630058·,·0.6336629·], | |
| 148 | ·······[0.07506042,·0.25881794,·0.2790243·], | ||
| 149 | ·······[0.7146926·,·0.37712127,·0.8139112·], | ||
| 150 | ·······[0.76515955,·0.8881079·,·0.290039··], | ||
| 151 | ·······[0.9350002·,·0.7703131·,·0.98512655], | ||
| 152 | ·······[0.52404183,·0.5848071·,·0.93785363], | ||
| 153 | ·······[0.11575463,·0.48285633,·0.03564102]],·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, 69 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 | ········"922 | 816 | ········"19622535":·8, |
| 817 | ········"22633724":·8, | ||
| 818 | ········"07840342":·8, | ||
| 819 | ········" | 817 | ········"10364336":·8, |
| 820 | ········" | 818 | ········"73504":·8, |
| 821 | ········"44016424":·8, | ||
| 822 | ········"4 | 819 | ········"42037013":·8, |
| 820 | ········"12902392":·8, | ||
| 823 | ········" | 821 | ········"12509118":·8, |
| 824 | ········"3869858":·8, | ||
| 825 | ········"6653195":·8, | ||
| 826 | ········"40534142":·8, | ||
| 827 | ········"89931124":·8, | ||
| 828 | ········"09279376":·8, | ||
| 829 | ········"57808363":·8, | ||
| 830 | ········"6925787":·8, | ||
| 831 | ········"34779903":·8, | ||
| 832 | ········"69938034":·8, | ||
| 833 | ········"3338973":·8, | ||
| 834 | ········" | 822 | ········"85473853":·8, |
| 823 | ········"4855717":·8, | ||
| 835 | ········"254 | 824 | ········"2546638":·8, |
| 836 | ········"20324644":·8, | ||
| 837 | ········" | 825 | ········"03070883":·8, |
| 826 | ········"9847538":·8, | ||
| 838 | ········" | 827 | ········"9913866":·8, |
| 839 | ········" | 828 | ········"36848673":·8, |
| 840 | ········"75765216":·8, | ||
| 841 | ········" | 829 | ········"88404053":·8, |
| 842 | ········"8 | 830 | ········"8322486":·8, |
| 831 | ········"26584858":·8, | ||
| 832 | ········"26227":·8, | ||
| 833 | ········"3523023":·8, | ||
| 834 | ········"5500672":·8, | ||
| 835 | ········"7017762":·8, | ||
| 836 | ········"21717823":·8, | ||
| 837 | ········"0484382":·8, | ||
| 838 | ········"25592637":·8, | ||
| 839 | ········"83795255":·8, | ||
| 840 | ········"31152233":·8, | ||
| 841 | ········"53387904":·8, | ||
| 842 | ········"95502675":·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 | ········"7918157e":·8, | ||
| 848 | ········"01":·8, | ||
| 849 | ········"8956065e":·8, | ||
| 850 | ········" | 847 | ········"23688282":·8, |
| 851 | ········" | 848 | ········"9630058":·8, |
| 852 | ········"9359033e":·8, | ||
| 853 | ········"1214675e":·8, | ||
| 854 | ········"8658469e":·8, | ||
| 855 | ········"3486205e":·8, | ||
| 856 | ········" | 849 | ········"6336629":·8, |
| 857 | ········" | 850 | ········"07506042":·8, |
| 851 | ········"25881794":·8, | ||
| 858 | ········"02":·8, | 852 | ········"2790243":·8, |
| 859 | ········"5347688e":·8, | ||
| 860 | ········"0949745e":·8, | ||
| 861 | ········"7 | 853 | ········"7146926":·8, |
| 862 | ········" | 854 | ········"37712127":·8, |
| 855 | ········"8139112":·8, | ||
| 856 | ········"76515955":·8, | ||
| 857 | ········"8881079":·8, | ||
| 863 | ········" | 858 | ········"290039":·8, |
| 864 | ········"9934774e":·8, | ||
| 865 | ········" | 859 | ········"9350002":·8, |
| 866 | ········"4514567e":·8, | ||
| 867 | ········" | 860 | ········"7703131":·8, |
| 861 | ········"98512655":·8, | ||
| 868 | ········"04":·8, | 862 | ········"52404183":·8, |
| 863 | ········"5848071":·8, | ||
| 869 | ········" | 864 | ········"93785363":·8, |
| 870 | ········" | 865 | ········"11575463":·8, |
| 866 | ········"48285633":·8, | ||
| 867 | ········"03564102":·8, | ||
| 871 | ········"It":·[8,·13,·16,·17], | 868 | ········"It":·[8,·13,·16,·17], |
| 872 | ········"like":·[8,·14,·16], | 869 | ········"like":·[8,·14,·16], |
| 873 | ········"grid":·[8,·16], | 870 | ········"grid":·[8,·16], |
| 874 | ········"over":·[8,·15], | 871 | ········"over":·[8,·15], |
| 875 | ········"internet":·[8,·11], | 872 | ········"internet":·[8,·11], |
| 876 | ········"slow":·8, | 873 | ········"slow":·8, |
| 877 | ········"whenev":·8, | 874 | ········"whenev":·8, |