Update Doxygen docs.

docs/annotated_dup.js

@@ -156,6 +156,11 @@ var annotated_dup =
     [ "gmres_lib", null, [
       [ "gmres_info", "structgmres__lib_1_1gmres__info.html", "structgmres__lib_1_1gmres__info" ]
     ] ],
+    [ "gradient_descent", "namespacegradient__descent.html", [
+      [ "gradient_descent_class", "structgradient__descent_1_1gradient__descent__class.html", "structgradient__descent_1_1gradient__descent__class" ],
+      [ "gradient_descent_test_class", "structgradient__descent_1_1gradient__descent__test__class.html", "structgradient__descent_1_1gradient__descent__test__class" ],
+      [ "check", "interfacegradient__descent_1_1check.html", "interfacegradient__descent_1_1check" ]
+    ] ],
     [ "guassian_process", "namespaceguassian__process.html", [
       [ "gaussp_class", "structguassian__process_1_1gaussp__class.html", "structguassian__process_1_1gaussp__class" ],
       [ "gaussp_class_pointer", "structguassian__process_1_1gaussp__class__pointer.html", "structguassian__process_1_1gaussp__class__pointer" ]

docs/dir_afec52aeb71f34b3b73b56ec632700cc.html

@@ -98,6 +98,9 @@
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 <tr class="memdesc:file__opts_8f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Contains module <a class="el" href="namespacefile__opts.html">file_opts</a>. <br /></td></tr>
 <tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:gradient__descent_8f"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gradient__descent_8f.html">gradient_descent.f</a></td></tr>
+<tr class="memdesc:gradient__descent_8f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Contains module <a class="el" href="namespacegradient__descent.html">gradient_descent</a>. <br /></td></tr>
+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:integration__path_8f"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="integration__path_8f.html">integration_path.f</a></td></tr>
 <tr class="memdesc:integration__path_8f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Contains module <a class="el" href="namespaceintegration__path.html">integration_path</a>. <br /></td></tr>
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docs/dir_afec52aeb71f34b3b73b56ec632700cc.js

@@ -3,6 +3,7 @@ var dir_afec52aeb71f34b3b73b56ec632700cc =
     [ "compression.f", "compression_8f.html", "compression_8f" ],
     [ "coordinate_utilities.f", "coordinate__utilities_8f.html", "coordinate__utilities_8f" ],
     [ "file_opts.f", "file__opts_8f.html", "file__opts_8f" ],
+    [ "gradient_descent.f", "gradient__descent_8f.html", "gradient__descent_8f" ],
     [ "integration_path.f", "integration__path_8f.html", "integration__path_8f" ],
     [ "integration_path_context.f", "integration__path__context_8f.html", [
       [ "integration_path_context_class", "structintegration__path__context_1_1integration__path__context__class.html", "structintegration__path__context_1_1integration__path__context__class" ],

docs/files.html

@@ -117,12 +117,13 @@
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 <tr id="row_2_0_3_1_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="coordinate__utilities_8f.html" target="_self">coordinate_utilities.f</a></td><td class="desc">Contains module <a class="el" href="namespacecoordinate__utilities.html">coordinate_utilities</a> </td></tr>
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-<tr id="row_2_0_3_3_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="integration__path_8f.html" target="_self">integration_path.f</a></td><td class="desc">Contains module <a class="el" href="namespaceintegration__path.html">integration_path</a> </td></tr>
-<tr id="row_2_0_3_4_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="integration__path__context_8f.html" target="_self">integration_path_context.f</a></td><td class="desc">Contains module <a class="el" href="namespaceintegration__path__context.html">integration_path_context</a> </td></tr>
-<tr id="row_2_0_3_5_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="magnetic__response_8f.html" target="_self">magnetic_response.f</a></td><td class="desc">Contains module <a class="el" href="namespacemagnetic__response.html">magnetic_response</a> </td></tr>
-<tr id="row_2_0_3_6_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="mpi__inc_8f.html" target="_self">mpi_inc.f</a></td><td class="desc">Contains module <a class="el" href="namespacempi__inc.html">mpi_inc</a> </td></tr>
-<tr id="row_2_0_3_7_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="profiler_8f.html" target="_self">profiler.f</a></td><td class="desc">Contains module <a class="el" href="namespaceprofiler.html">profiler</a> </td></tr>
-<tr id="row_2_0_3_8_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="vmec__input_8f.html" target="_self">vmec_input.f</a></td><td class="desc">Contains the module <a class="el" href="namespacevmec__input.html">vmec_input</a> </td></tr>
+<tr id="row_2_0_3_3_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="gradient__descent_8f.html" target="_self">gradient_descent.f</a></td><td class="desc">Contains module <a class="el" href="namespacegradient__descent.html">gradient_descent</a> </td></tr>
+<tr id="row_2_0_3_4_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="integration__path_8f.html" target="_self">integration_path.f</a></td><td class="desc">Contains module <a class="el" href="namespaceintegration__path.html">integration_path</a> </td></tr>
+<tr id="row_2_0_3_5_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="integration__path__context_8f.html" target="_self">integration_path_context.f</a></td><td class="desc">Contains module <a class="el" href="namespaceintegration__path__context.html">integration_path_context</a> </td></tr>
+<tr id="row_2_0_3_6_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="magnetic__response_8f.html" target="_self">magnetic_response.f</a></td><td class="desc">Contains module <a class="el" href="namespacemagnetic__response.html">magnetic_response</a> </td></tr>
+<tr id="row_2_0_3_7_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="mpi__inc_8f.html" target="_self">mpi_inc.f</a></td><td class="desc">Contains module <a class="el" href="namespacempi__inc.html">mpi_inc</a> </td></tr>
+<tr id="row_2_0_3_8_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="profiler_8f.html" target="_self">profiler.f</a></td><td class="desc">Contains module <a class="el" href="namespaceprofiler.html">profiler</a> </td></tr>
+<tr id="row_2_0_3_9_" class="even" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="vmec__input_8f.html" target="_self">vmec_input.f</a></td><td class="desc">Contains the module <a class="el" href="namespacevmec__input.html">vmec_input</a> </td></tr>
 <tr id="row_2_1_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span id="arr_2_1_" class="arrow" onclick="toggleFolder('2_1_')">&#9658;</span><span id="img_2_1_" class="iconfclosed" onclick="toggleFolder('2_1_')">&#160;</span><a class="el" href="dir_91ae10d308d664685908361c265faa14.html" target="_self">Testing</a></td><td class="desc"></td></tr>
 <tr id="row_2_1_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span id="arr_2_1_0_" class="arrow" onclick="toggleFolder('2_1_0_')">&#9658;</span><span id="img_2_1_0_" class="iconfclosed" onclick="toggleFolder('2_1_0_')">&#160;</span><a class="el" href="dir_df688ec02258136ac174dc4fd02d25b5.html" target="_self">test_utilities</a></td><td class="desc"></td></tr>
 <tr id="row_2_1_0_0_" style="display:none;"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="file__opts__tester_8f.html" target="_self">file_opts_tester.f</a></td><td class="desc">Utility to run the file opts operations </td></tr>

docs/functions_c.html

@@ -101,13 +101,15 @@ <h3><a id="index_c"></a>- c -</h3><ul>
 : <a class="el" href="interfaceintegration__path_1_1check.html#a28399e5d62c4d80adc58f10ed95cbd58">integration_path::check</a>
 </li>
 <li>check_log()
-: <a class="el" href="interfaceintegration__path_1_1check.html#a8614af2194990fc83b852b1e7b9cb13c">integration_path::check</a>
+: <a class="el" href="interfacegradient__descent_1_1check.html#a96bcd76504775923cfa93cad7787137c">gradient_descent::check</a>
+, <a class="el" href="interfaceintegration__path_1_1check.html#a8614af2194990fc83b852b1e7b9cb13c">integration_path::check</a>
 </li>
 <li>check_mn()
 : <a class="el" href="interfacefourier_1_1check.html#a44be69f7942c9a087dc61605220df356">fourier::check</a>
 </li>
 <li>check_real()
-: <a class="el" href="interfaceintegration__path_1_1check.html#a2f08df4b2a994b3588e63af14d948d55">integration_path::check</a>
+: <a class="el" href="interfacegradient__descent_1_1check.html#ace6dd917b6b2238940f4de7518c124a9">gradient_descent::check</a>
+, <a class="el" href="interfaceintegration__path_1_1check.html#a2f08df4b2a994b3588e63af14d948d55">integration_path::check</a>
 </li>
 <li>chipf
 : <a class="el" href="classsiesta__quantities.html#a6d46c1f2cc589a9a30cd2961396a9d16">siesta_quantities</a>

docs/functions_func_c.html

@@ -95,13 +95,15 @@ <h3><a id="index_c"></a>- c -</h3><ul>
 : <a class="el" href="interfaceintegration__path_1_1check.html#a28399e5d62c4d80adc58f10ed95cbd58">integration_path::check</a>
 </li>
 <li>check_log()
-: <a class="el" href="interfaceintegration__path_1_1check.html#a8614af2194990fc83b852b1e7b9cb13c">integration_path::check</a>
+: <a class="el" href="interfacegradient__descent_1_1check.html#a96bcd76504775923cfa93cad7787137c">gradient_descent::check</a>
+, <a class="el" href="interfaceintegration__path_1_1check.html#a8614af2194990fc83b852b1e7b9cb13c">integration_path::check</a>
 </li>
 <li>check_mn()
 : <a class="el" href="interfacefourier_1_1check.html#a44be69f7942c9a087dc61605220df356">fourier::check</a>
 </li>
 <li>check_real()
-: <a class="el" href="interfaceintegration__path_1_1check.html#a2f08df4b2a994b3588e63af14d948d55">integration_path::check</a>
+: <a class="el" href="interfacegradient__descent_1_1check.html#ace6dd917b6b2238940f4de7518c124a9">gradient_descent::check</a>
+, <a class="el" href="interfaceintegration__path_1_1check.html#a2f08df4b2a994b3588e63af14d948d55">integration_path::check</a>
 </li>
 <li>combination_construct()
 : <a class="el" href="structcombination_1_1combination__class.html#a63bdead59d722c73519f32eb08356784">combination::combination_class</a>

docs/functions_func_g.html

@@ -243,6 +243,9 @@ <h3><a id="index_g"></a>- g -</h3><ul>
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 , <a class="el" href="classvmec__quantities.html#afc5686dd846f6ac420931e03c13a0f8d">vmec_quantities</a>
 </li>
+<li>gradient_descent_test_construct()
+: <a class="el" href="structgradient__descent_1_1gradient__descent__test__class.html#a1e09a99f5993896bcb9087a9e632e517">gradient_descent::gradient_descent_test_class</a>
+</li>
 <li>gradienthalf()
 : <a class="el" href="interfaceutilities_1_1gradienthalf.html#a09e6db5e1b08df84f065b2c2a7ab9ecd">utilities::gradienthalf</a>
 </li>

docs/functions_g.html

@@ -255,6 +255,9 @@ <h3><a id="index_g"></a>- g -</h3><ul>
 <li>gradient
 : <a class="el" href="structreconstruction_1_1reconstruction__class.html#ae77f2ddb1c385fd13fd5e9f39325e448">reconstruction::reconstruction_class</a>
 </li>
+<li>gradient_descent_test_construct()
+: <a class="el" href="structgradient__descent_1_1gradient__descent__test__class.html#a1e09a99f5993896bcb9087a9e632e517">gradient_descent::gradient_descent_test_class</a>
+</li>
 <li>gradienthalf()
 : <a class="el" href="interfaceutilities_1_1gradienthalf.html#a09e6db5e1b08df84f065b2c2a7ab9ecd">utilities::gradienthalf</a>
 </li>

docs/functions_s.html

@@ -176,6 +176,9 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 <li>state_flags
 : <a class="el" href="structmodel_1_1model__class.html#a3385fb1d7d2f4ead045e7f46fc34ec78">model::model_class</a>
 </li>
+<li>step
+: <a class="el" href="structgradient__descent_1_1gradient__descent__class.html#a491389485ae29548abfe67bfc3e08dce">gradient_descent::gradient_descent_class</a>
+</li>
 <li>step_max
 : <a class="el" href="structreconstruction_1_1reconstruction__class.html#a0ad3027403a902a95641d57854e6b51b">reconstruction::reconstruction_class</a>
 </li>

docs/functions_t.html

@@ -156,7 +156,10 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 </li>
 <li>to_prime()
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-, <a class="el" href="classvmec__quantities.html#a803e2f4f2a6c22379a109da6533880ef">vmec_quantities</a>
+, <a class="el" href="classvmec__quantities.html#ac395b16cc877af1062e6b13341f0b5b9">vmec_quantities</a>
+</li>
+<li>tolarance
+: <a class="el" href="structgradient__descent_1_1gradient__descent__class.html#a8ab2937173b456ea90cf19658048f886">gradient_descent::gradient_descent_class</a>
 </li>
 <li>tolerance
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docs/functions_vars_s.html

@@ -146,6 +146,9 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 <li>state_flags
 : <a class="el" href="structmodel_1_1model__class.html#a3385fb1d7d2f4ead045e7f46fc34ec78">model::model_class</a>
 </li>
+<li>step
+: <a class="el" href="structgradient__descent_1_1gradient__descent__class.html#a491389485ae29548abfe67bfc3e08dce">gradient_descent::gradient_descent_class</a>
+</li>
 <li>step_max
 : <a class="el" href="structreconstruction_1_1reconstruction__class.html#a0ad3027403a902a95641d57854e6b51b">reconstruction::reconstruction_class</a>
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docs/functions_vars_t.html

@@ -133,6 +133,9 @@ <h3><a id="index_t"></a>- t -</h3><ul>
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 </li>
+<li>tolarance
+: <a class="el" href="structgradient__descent_1_1gradient__descent__class.html#a8ab2937173b456ea90cf19658048f886">gradient_descent::gradient_descent_class</a>
+</li>
 <li>tolerance
 : <a class="el" href="structguassian__process_1_1gaussp__class.html#abbc1968221ec576c536a062a48f910f1">guassian_process::gaussp_class</a>
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docs/functions_vars_x.html

@@ -99,6 +99,9 @@ <h3><a id="index_x"></a>- x -</h3><ul>
 <li>x_prime
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 </li>
+<li>x_var
+: <a class="el" href="structgradient__descent_1_1gradient__descent__class.html#a56754f3b3c2e8760a066c6caf120206d">gradient_descent::gradient_descent_class</a>
+</li>
 <li>xc
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docs/functions_x.html

@@ -102,6 +102,9 @@ <h3><a id="index_x"></a>- x -</h3><ul>
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 </li>
+<li>x_var
+: <a class="el" href="structgradient__descent_1_1gradient__descent__class.html#a56754f3b3c2e8760a066c6caf120206d">gradient_descent::gradient_descent_class</a>
+</li>
 <li>xc
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