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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([[0.7464663·,·0.95336473,·0.7646863·],</span> |
| 199 | <span·class="go">·······[0. | 199 | <span·class="go">·······[0.9766425·,·0.39678612,·0.60779697],</span> |
| 200 | <span·class="go">·······[0.89620507,·0.4377872·,·0.5764169·],</span> | ||
| 200 | <span·class="go">·······[0. | 201 | <span·class="go">·······[0.83945996,·0.5443509·,·0.40876678],</span> |
| 201 | <span·class="go">·······[0.36397937,·0.06778045,·0.696222··],</span> | ||
| 202 | <span·class="go">·······[0.5 | 202 | <span·class="go">·······[0.5226231·,·0.17476153,·0.30245203],</span> |
| 203 | <span·class="go">·······[0.51583683,·0.2748747·,·0.03980057],</span> | ||
| 203 | <span·class="go">·······[0. | 204 | <span·class="go">·······[0.8133657·,·0.733752··,·0.74457335],</span> |
| 204 | <span·class="go">·······[0. | 205 | <span·class="go">·······[0.4288136·,·0.51777613,·0.47890168],</span> |
| 205 | <span·class="go">·······[0.33926526,·0.89014286,·0.16976635],</span> | ||
| 206 | <span·class="go">·······[0.3 | 206 | <span·class="go">·······[0.3874723·,·0.8482516·,·0.58224165]],·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. | 241 | <span·class="go">array([[0.5690155·,·0.5727605·,·0.22527999],</span> |
| 242 | <span·class="go">·······[0.9919063·,·0.23359638,·0.5809065·],</span> | ||
| 243 | <span·class="go">·······[0.85974574,·0.7840573·,·0.70808566],</span> | ||
| 242 | <span·class="go">·······[0. | 244 | <span·class="go">·······[0.7786572·,·0.01189263,·0.8535928·],</span> |
| 243 | <span·class="go">·······[0.03169398,·0.37426385,·0.10960583],</span> | ||
| 244 | <span·class="go">·······[0.5062379·,·0.37031758,·0.26156208],</span> | ||
| 245 | <span·class="go">·······[0.9 | 245 | <span·class="go">·······[0.9105352·,·0.59369504,·0.4310235·],</span> |
| 246 | <span·class="go">·······[0. | 246 | <span·class="go">·······[0.4164023·,·0.8897345·,·0.58014494],</span> |
| 247 | <span·class="go">·······[0. | 247 | <span·class="go">·······[0.71285105,·0.9805963·,·0.11398367]],·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([[0.66548145,·0.7217738·,·0.3356938·], | ||
| 111 | ·······[0.5118772·,·0.31913754,·0.8520619·], | ||
| 112 | ·······[0.13728406,·0.86236···,·0.05703682], | ||
| 113 | ·······[0.36397937,·0.06778045,·0.696222··], | ||
| 114 | ·······[0.5390319·,·0.65108067,·0.65739554], | ||
| 115 | ·······[0.9344352·,·0.9795785·,·0.68341315], | ||
| 116 | ·······[0.5518626·,·0.9389614·,·0.4589597·], | ||
| 117 | ·······[0.33926526,·0.89014286,·0.16976635], | ||
| 118 | 110 | array([[0.7464663·,·0.95336473,·0.7646863·], | |
| 111 | ·······[0.9766425·,·0.39678612,·0.60779697], | ||
| 112 | ·······[0.89620507,·0.4377872·,·0.5764169·], | ||
| 113 | ·······[0.83945996,·0.5443509·,·0.40876678], | ||
| 114 | ·······[0.5226231·,·0.17476153,·0.30245203], | ||
| 115 | ·······[0.51583683,·0.2748747·,·0.03980057], | ||
| 116 | ·······[0.8133657·,·0.733752··,·0.74457335], | ||
| 117 | ·······[0.4288136·,·0.51777613,·0.47890168], | ||
| 118 | ·······[0.3874723·,·0.8482516·,·0.58224165]],·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([[0.6602933·,·0.04728471,·0.00328238], | ||
| 148 | ·······[0.5826964·,·0.8271196·,·0.5300329·], | ||
| 149 | ·······[0.03169398,·0.37426385,·0.10960583], | ||
| 150 | ·······[0.5062379·,·0.37031758,·0.26156208], | ||
| 151 | ·······[0.9803024·,·0.5835559·,·0.9713085·], | ||
| 152 | 147 | array([[0.5690155·,·0.5727605·,·0.22527999], | |
| 148 | ·······[0.9919063·,·0.23359638,·0.5809065·], | ||
| 149 | ·······[0.85974574,·0.7840573·,·0.70808566], | ||
| 150 | ·······[0.7786572·,·0.01189263,·0.8535928·], | ||
| 151 | ·······[0.9105352·,·0.59369504,·0.4310235·], | ||
| 152 | ·······[0.4164023·,·0.8897345·,·0.58014494], | ||
| 153 | ·······[0. | 153 | ·······[0.71285105,·0.9805963·,·0.11398367]],·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 | ········"66548145":·8, | ||
| 817 | ········"7 | 816 | ········"7464663":·8, |
| 818 | ········" | 817 | ········"95336473":·8, |
| 819 | ········"5118772":·8, | ||
| 820 | ········"31913754":·8, | ||
| 821 | ········"8520619":·8, | ||
| 822 | ········"13728406":·8, | ||
| 823 | ········" | 818 | ········"7646863":·8, |
| 824 | ········"05703682":·8, | ||
| 825 | ········"36397937":·8, | ||
| 826 | ········"06778045":·8, | ||
| 827 | ········"696222":·8, | ||
| 828 | ········"5390319":·8, | ||
| 829 | ········"65108067":·8, | ||
| 830 | ········"65739554":·8, | ||
| 831 | ········"9344352":·8, | ||
| 832 | ········"9795785":·8, | ||
| 833 | ········"68341315":·8, | ||
| 834 | ········"5518626":·8, | ||
| 835 | ········"9389614":·8, | ||
| 836 | ········"4589597":·8, | ||
| 837 | ········"33926526":·8, | ||
| 838 | ········"89014286":·8, | ||
| 839 | ········" | 819 | ········"9766425":·8, |
| 820 | ········"39678612":·8, | ||
| 821 | ········"60779697":·8, | ||
| 822 | ········"89620507":·8, | ||
| 823 | ········"4377872":·8, | ||
| 824 | ········"5764169":·8, | ||
| 825 | ········"83945996":·8, | ||
| 826 | ········"5443509":·8, | ||
| 827 | ········"40876678":·8, | ||
| 828 | ········"5226231":·8, | ||
| 829 | ········"17476153":·8, | ||
| 830 | ········"30245203":·8, | ||
| 831 | ········"51583683":·8, | ||
| 832 | ········"2748747":·8, | ||
| 833 | ········"03980057":·8, | ||
| 834 | ········"8133657":·8, | ||
| 835 | ········"733752":·8, | ||
| 836 | ········"74457335":·8, | ||
| 840 | ········" | 837 | ········"4288136":·8, |
| 838 | ········"51777613":·8, | ||
| 839 | ········"47890168":·8, | ||
| 841 | ········" | 840 | ········"3874723":·8, |
| 842 | ········" | 841 | ········"8482516":·8, |
| 842 | ········"58224165":·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 | ········"6602933":·8, | ||
| 848 | ········"04728471":·8, | ||
| 849 | ········"00328238":·8, | ||
| 850 | ········"5 | 847 | ········"5690155":·8, |
| 851 | ········"8271196":·8, | ||
| 852 | ········"5300329":·8, | ||
| 853 | ········"03169398":·8, | ||
| 854 | ········" | 848 | ········"5727605":·8, |
| 855 | ········"10960583":·8, | ||
| 856 | ········" | 849 | ········"22527999":·8, |
| 850 | ········"9919063":·8, | ||
| 857 | ········" | 851 | ········"23359638":·8, |
| 858 | ········"26156208":·8, | ||
| 859 | ········" | 852 | ········"5809065":·8, |
| 853 | ········"85974574":·8, | ||
| 854 | ········"7840573":·8, | ||
| 855 | ········"70808566":·8, | ||
| 856 | ········"7786572":·8, | ||
| 857 | ········"01189263":·8, | ||
| 860 | ········" | 858 | ········"8535928":·8, |
| 861 | ········"9 | 859 | ········"9105352":·8, |
| 862 | ········" | 860 | ········"59369504":·8, |
| 861 | ········"4310235":·8, | ||
| 863 | ········"4 | 862 | ········"4164023":·8, |
| 864 | ········"34112296":·8, | ||
| 865 | ········"8 | 863 | ········"8897345":·8, |
| 866 | ········" | 864 | ········"58014494":·8, |
| 865 | ········"71285105":·8, | ||
| 866 | ········"9805963":·8, | ||
| 867 | ········"3 | 867 | ········"11398367":·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, |