-
Notifications
You must be signed in to change notification settings - Fork 0
/
Quick start.html
313 lines (196 loc) · 14 KB
/
Quick start.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Quick start — AGAT 2022.10.04 documentation</title>
<script type="text/javascript" src="_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Brief" href="Tutorial.html" />
<link rel="prev" title="Installation" href="Installation.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home"> AGAT
<img src="_static/logo.svg" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<p class="caption" role="heading"><span class="caption-text">AGAT:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Installation.html">Installation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Quick start</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#prepare-vasp-calculations">Prepare VASP calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#collect-paths-of-vasp-calculations">Collect paths of VASP calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#build-database">Build database</a></li>
<li class="toctree-l2"><a class="reference internal" href="#train-agat-model">Train AGAT model</a></li>
<li class="toctree-l2"><a class="reference internal" href="#application-geometry-optimization">Application (geometry optimization)</a></li>
<li class="toctree-l2"><a class="reference internal" href="#application-high-throughput-prediction">Application (high-throughput prediction)</a></li>
</ul>
</li>
</ul>
<p class="caption" role="heading"><span class="caption-text">AGAT Tutorial:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Tutorial.html">Brief</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tutorial.html#more-tutorials">More tutorials</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">中文手册:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Chinese_support.html">中文手册</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">AGAT API:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="API_Docs.html">API_Docs</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">OTHER:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="Contribution.html">Contribution</a></li>
<li class="toctree-l1"><a class="reference internal" href="Reference.html">Reference</a></li>
<li class="toctree-l1"><a class="reference internal" href="FAQ.html">Frequently asked questions (FAQ)</a></li>
<li class="toctree-l1"><a class="reference internal" href="Change_log.html">Change log</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">AGAT</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html">Docs</a> »</li>
<li>Quick start</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/Quick start.md.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="quick-start">
<h1>Quick start<a class="headerlink" href="#quick-start" title="Permalink to this heading">¶</a></h1>
<section id="prepare-vasp-calculations">
<h2>Prepare VASP calculations<a class="headerlink" href="#prepare-vasp-calculations" title="Permalink to this heading">¶</a></h2>
<p>Run VASP calculations at this step.</p>
</section>
<section id="collect-paths-of-vasp-calculations">
<h2>Collect paths of VASP calculations<a class="headerlink" href="#collect-paths-of-vasp-calculations" title="Permalink to this heading">¶</a></h2>
<ul>
<li><p>We provided examples of VASP outputs at <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v1.0.0/files/VASP_calculations_example">VASP_calculations_example</a>.</p></li>
<li><p>Find all directories containing <code class="docutils literal notranslate"><span class="pre">OUTCAR</span></code> file:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">find</span> <span class="o">.</span> <span class="o">-</span><span class="n">name</span> <span class="n">OUTCAR</span> <span class="o">></span> <span class="n">paths</span><span class="o">.</span><span class="n">log</span>
</pre></div>
</div>
</li>
<li><p>Remove the string ‘OUTCAR’ in <code class="docutils literal notranslate"><span class="pre">paths.log</span></code>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sed</span> <span class="o">-</span><span class="n">i</span> <span class="s1">'s/OUTCAR$//g'</span> <span class="n">paths</span><span class="o">.</span><span class="n">log</span>
</pre></div>
</div>
</li>
<li><p>Specify the absolute paths in <code class="docutils literal notranslate"><span class="pre">paths.log</span></code>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sed</span> <span class="o">-</span><span class="n">i</span> <span class="s2">"s#^.#$</span><span class="si">{PWD}</span><span class="s2">#g"</span> <span class="n">paths</span><span class="o">.</span><span class="n">log</span>
</pre></div>
</div>
</li>
</ul>
</section>
<section id="build-database">
<h2>Build database<a class="headerlink" href="#build-database" title="Permalink to this heading">¶</a></h2>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">agat.data</span> <span class="kn">import</span> <span class="n">BuildDatabase</span>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">'__main__'</span><span class="p">:</span>
<span class="n">database</span> <span class="o">=</span> <span class="n">BuildDatabase</span><span class="p">(</span><span class="n">mode_of_NN</span><span class="o">=</span><span class="s1">'ase_dist'</span><span class="p">,</span> <span class="n">num_of_cores</span><span class="o">=</span><span class="mi">16</span><span class="p">)</span>
<span class="n">database</span><span class="o">.</span><span class="n">build</span><span class="p">()</span>
</pre></div>
</div>
</section>
<section id="train-agat-model">
<h2>Train AGAT model<a class="headerlink" href="#train-agat-model" title="Permalink to this heading">¶</a></h2>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">agat.model</span> <span class="kn">import</span> <span class="n">Fit</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">Fit</span><span class="p">()</span>
<span class="n">f</span><span class="o">.</span><span class="n">fit</span><span class="p">()</span>
</pre></div>
</div>
</section>
<section id="application-geometry-optimization">
<h2>Application (geometry optimization)<a class="headerlink" href="#application-geometry-optimization" title="Permalink to this heading">¶</a></h2>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ase.optimize</span> <span class="kn">import</span> <span class="n">BFGS</span>
<span class="kn">from</span> <span class="nn">ase.io</span> <span class="kn">import</span> <span class="n">read</span>
<span class="kn">from</span> <span class="nn">agat.app</span> <span class="kn">import</span> <span class="n">AgatCalculator</span>
<span class="n">model_save_dir</span> <span class="o">=</span> <span class="s1">'agat_model'</span>
<span class="n">graph_build_scheme_dir</span> <span class="o">=</span> <span class="s1">'dataset'</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">read</span><span class="p">(</span><span class="s1">'POSCAR'</span><span class="p">)</span>
<span class="n">calculator</span><span class="o">=</span><span class="n">AgatCalculator</span><span class="p">(</span><span class="n">model_save_dir</span><span class="p">,</span>
<span class="n">graph_build_scheme_dir</span><span class="p">)</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">Atoms</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">calculator</span><span class="o">=</span><span class="n">calculator</span><span class="p">)</span>
<span class="n">dyn</span> <span class="o">=</span> <span class="n">BFGS</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">trajectory</span><span class="o">=</span><span class="s1">'test.traj'</span><span class="p">)</span>
<span class="n">dyn</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">fmax</span><span class="o">=</span><span class="mf">0.05</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="application-high-throughput-prediction">
<h2>Application (high-throughput prediction)<a class="headerlink" href="#application-high-throughput-prediction" title="Permalink to this heading">¶</a></h2>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">agat.app.cata</span> <span class="kn">import</span> <span class="n">HtAds</span>
<span class="n">model_save_dir</span> <span class="o">=</span> <span class="s1">'agat_model'</span>
<span class="n">graph_build_scheme_dir</span> <span class="o">=</span> <span class="s1">'dataset'</span>
<span class="n">formula</span><span class="o">=</span><span class="s1">'NiCoFePdPt'</span>
<span class="n">ha</span> <span class="o">=</span> <span class="n">HtAds</span><span class="p">(</span><span class="n">model_save_dir</span><span class="o">=</span><span class="n">model_save_dir</span><span class="p">,</span> <span class="n">graph_build_scheme_dir</span><span class="o">=</span><span class="n">graph_build_scheme_dir</span><span class="p">)</span>
<span class="n">ha</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">formula</span><span class="o">=</span><span class="n">formula</span><span class="p">)</span>
</pre></div>
</div>
</section>
</section>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="Tutorial.html" class="btn btn-neutral float-right" title="Brief" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="Installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>
© Copyright 2023, ZHANG Jun, ZHAO Shijun
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>