https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Command%3A_gradient 2026-04-09T18:30:48Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Command:_gradient&diff=6751&oldid=prev 2009-08-07T12:06:15Z

<p><span class="autocomment">Description</span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:06, 7 August 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Description ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Description ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">This function computes </del>the gradient, i.e. the partial derivatives</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Computes </ins>the gradient, i.e. the partial derivatives of the target function against the torsion angle, numerically and compares the result with the gradient computed by the (normal) analytic method. The numerical derivatives are calculated with the given ''step'' <ins style="font-weight: bold; text-decoration: none;">size given</ins>, as well as <ins style="font-weight: bold; text-decoration: none;">with </ins>a 10 times smaller and a 10 times larger step size. The deviation of the analytical gradient from the three numerically calculated gradient values are reported for all torsion angles for which the maximal absolute deviation exceeds the <ins style="font-weight: bold; text-decoration: none;">given </ins>''cutoff'' <ins style="font-weight: bold; text-decoration: none;">value</ins>.</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>of the target function against the torsion angle, numerically and</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This command is useful to check the analytical gradient calculation for correctness after a change <ins style="font-weight: bold; text-decoration: none;">to the implementation </ins>of the target function and<ins style="font-weight: bold; text-decoration: none;">/or </ins>gradient calculation.</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>compares the result with the gradient computed by the (normal)</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>analytic method. The numerical derivatives are calculated with the</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">step size </del>given <del style="font-weight: bold; text-decoration: none;">by the '</del>''step''<del style="font-weight: bold; text-decoration: none;">' parameter</del>, as well as <del style="font-weight: bold; text-decoration: none;">by using </del>a 10</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>times smaller and a 10 times larger step size. The deviation of the</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>analytical gradient from the three numerically calculated gradient</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>values are reported for all torsion angles for which the maximal</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>absolute deviation exceeds the <del style="font-weight: bold; text-decoration: none;">value set by the '</del>''cutoff''<del style="font-weight: bold; text-decoration: none;">' parameter</del>.</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This command is useful to check the analytical gradient calculation</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>for correctness after a change of the target function and gradient</div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>calculation.</div></td><td colspan="2" class="diff-side-added"></td></tr> </table>

Masayo https://cyana.org/w/index.php?title=CYANA_Command:_gradient&diff=5354&oldid=prev 2009-01-29T11:26:55Z

<p>1 revision</p> <p><b>New page</b></p><div><br /> == Parameters ==<br /> <br /> ; step=&#039;&#039;real&#039;&#039;: (default: 0.000001)<br /> ; cutoff=&#039;&#039;real&#039;&#039;: (default: -1.0)<br /> <br /> == Description ==<br /> <br /> This function computes the gradient, i.e. the partial derivatives<br /> of the target function against the torsion angle, numerically and<br /> compares the result with the gradient computed by the (normal)<br /> analytic method. The numerical derivatives are calculated with the<br /> step size given by the &#039;&#039;&#039;step&#039;&#039;&#039; parameter, as well as by using a 10<br /> times smaller and a 10 times larger step size. The deviation of the<br /> analytical gradient from the three numerically calculated gradient<br /> values are reported for all torsion angles for which the maximal<br /> absolute deviation exceeds the value set by the &#039;&#039;&#039;cutoff&#039;&#039;&#039; parameter.<br /> <br /> This command is useful to check the analytical gradient calculation<br /> for correctness after a change of the target function and gradient<br /> calculation.</div>

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