forked from materialsproject/pymatgen
-
Notifications
You must be signed in to change notification settings - Fork 0
/
installation.html
620 lines (600 loc) · 48.5 KB
/
installation.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
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>Requirements — pymatgen 2019.5.1 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Overview" href="usage.html" />
<link rel="prev" title="Introduction" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33990148-1']);
_gaq.push(['_trackPageview']);
</script>
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
<a href="usage.html" title="Overview"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="index.html" title="Introduction"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">pymatgen 2019.5.1 documentation</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="requirements">
<h1>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h1>
<p>All required dependencies should be automatically taken care of if you
install pymatgen using easy_install or pip. Otherwise, these packages should
be available on <a class="reference external" href="http://pypi.python.org">PyPI</a>.</p>
<ol class="arabic simple">
<li><p>Python 2.7-3.x supported. <strong>It is highly recommended that you use latest
Python 3.x unless you know you need other dependencies that works with
Python 2.x only.</strong></p></li>
<li><p>numpy>=1.14</p></li>
<li><p>scipy>=1.0.1</p></li>
<li><p>matplotlib>=1.5+</p></li>
<li><p>monty>=0.9.6</p></li>
<li><p>requests>=2.0+</p></li>
<li><p>pybtex</p></li>
<li><p>pyyaml</p></li>
<li><p>tabulate</p></li>
<li><p>six</p></li>
</ol>
<p>Most of these are fairly easy to install. The well-established numpy and scipy
should have ready-made installation packages for all platforms. The rest are
pure/semi-pure Python packages that installs without any issues with pip and
easy_install.</p>
<div class="section" id="optional-dependencies">
<h2>Optional dependencies<a class="headerlink" href="#optional-dependencies" title="Permalink to this headline">¶</a></h2>
<p>Optional libraries that are required if you need certain features.</p>
<ol class="arabic simple">
<li><p>sympy: For defect generation and analysis.</p></li>
<li><p>VTK with Python bindings 5.8+ (<a class="reference external" href="http://www.vtk.org/">http://www.vtk.org/</a>): For visualization of
crystal structures using the pymatgen.vis package. Note that the VTK
package is incompatible with Python 3.x at the moment.</p></li>
<li><p>Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the
adapters in pymatgen.io.aseio between pymatgen’s core Structure object and
the Atoms object used by ASE. Get it at <a class="reference external" href="https://wiki.fysik.dtu.dk/ase/">https://wiki.fysik.dtu.dk/ase/</a>.
Note that the ASE package is incompatible with Python 3.x at the moment.</p></li>
<li><p>OpenBabel with Python bindings (<a class="reference external" href="http://openbabel.org">http://openbabel.org</a>): Required for the
usage of the adapters in pymatgen.io.babelio between pymatgen’s Molecule
and OpenBabel’s OBMol. Opens up input and output support for the very large
number of input and output formats supported by OpenBabel.</p></li>
<li><p>networkx: For graph analysis associated with critic2 topological analysis
of electron charge densities, pygraphviz is also required for visualization.</p></li>
<li><p>nose - For unittesting. Not optional for developers.</p></li>
</ol>
</div>
<div class="section" id="optional-non-python-programs">
<h2>Optional non-Python programs<a class="headerlink" href="#optional-non-python-programs" title="Permalink to this headline">¶</a></h2>
<p>Optional non-python libraries (because no good python alternative exists at
the moment) required only for certain features:</p>
<ol class="arabic simple">
<li><p>ffmpeg: For generation of movies in structure_vtk.py. The executable ffmpeg
must be in the path. Get it at <a class="reference external" href="http://www.ffmpeg.org">http://www.ffmpeg.org</a>.</p></li>
<li><p>enum: For the use of
<a class="reference internal" href="pymatgen.transformations.advanced_transformations.html#pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation" title="pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation</span></code></a>
and <a class="reference internal" href="pymatgen.command_line.enumlib_caller.html#module-pymatgen.command_line.enumlib_caller" title="pymatgen.command_line.enumlib_caller"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pymatgen.command_line.enumlib_caller</span></code></a> module. This library by Gus
Hart provides a robust way to enumerate derivative structures. It can be
used to completely enumerate all symmetrically distinct ordered structures
of disordered structures via EnumerateStructureTransformation. Many other
advanced transformations (e.g., MagOrderingTransformation) use
EnumerateStructureTransformation. The enum.x and makestr.x
executables must be in the path. Get it at <a class="reference external" href="http://enum.sourceforge.net">http://enum.sourceforge.net</a> and
follow the instructions to compile multienum.x and makestr.x.</p></li>
<li><p>bader: For use with <a class="reference internal" href="pymatgen.command_line.bader_caller.html#pymatgen.command_line.bader_caller.BaderAnalysis" title="pymatgen.command_line.bader_caller.BaderAnalysis"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.command_line.bader_caller.BaderAnalysis</span></code></a>.
This library by Henkelmann et al. provides a robust way to calculate the
Bader analysis from a CHGCAR. The bader executable must be in the path.
Get it at <a class="reference external" href="http://theory.cm.utexas.edu/bader">http://theory.cm.utexas.edu/bader</a>.</p></li>
<li><p>gulp: For use with <a class="reference internal" href="pymatgen.command_line.gulp_caller.html#module-pymatgen.command_line.gulp_caller" title="pymatgen.command_line.gulp_caller"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pymatgen.command_line.gulp_caller</span></code></a>,
which is in turn used extensively by <a class="reference internal" href="pymatgen.analysis.defects.html#module-pymatgen.analysis.defects" title="pymatgen.analysis.defects"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pymatgen.analysis.defects</span></code></a> to
compute empirical defect energies.</p></li>
<li><p>aconvasp: For use with the <a class="reference internal" href="pymatgen.command_line.aconvasp_caller.html#module-pymatgen.command_line.aconvasp_caller" title="pymatgen.command_line.aconvasp_caller"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pymatgen.command_line.aconvasp_caller</span></code></a>.</p></li>
<li><p>Zeo++ (<a class="reference external" href="http://zeoplusplus.org">http://zeoplusplus.org</a>): For defect structure
generation. This is required in addition to installing the zeo Python
package.</p></li>
<li><p>critic2 (<a class="reference external" href="https://github.com/aoterodelaroza/critic2">https://github.com/aoterodelaroza/critic2</a>): For topological
analysis of critical points from electronic charge density. Provides
more detailed information compared to bader. For use with
<a class="reference internal" href="pymatgen.command_line.critic2_caller.html#pymatgen.command_line.critic2_caller.Critic2Caller" title="pymatgen.command_line.critic2_caller.Critic2Caller"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.command_line.critic2_caller.Critic2Caller</span></code></a>.</p></li>
<li><p>graphviz (<a class="reference external" href="http://graphviz.org">http://graphviz.org</a>): For visualization of graphs generated
using critic2.</p></li>
</ol>
</div>
</div>
<div class="section" id="conda-based-install">
<h1>Conda-based install<a class="headerlink" href="#conda-based-install" title="Permalink to this headline">¶</a></h1>
<p>For these instructions, we will assume the <strong>64-bit</strong> versions of all OSes.
For OSX and Linux, both latest Python 3.x adn 2.7 are supported. For Windows,
only latest Python 3.x is supported. Most common functionality should work
out of the box on Windows, but some specialized analyses relying on external
programs may require you to compile those programs from source.</p>
<div class="section" id="step-1-install-conda">
<h2>Step 1: Install conda<a class="headerlink" href="#step-1-install-conda" title="Permalink to this headline">¶</a></h2>
<p>Download and install the version of conda for your operating system from
<a class="reference external" href="http://conda.pydata.org/miniconda.html">http://conda.pydata.org/miniconda.html</a>. For Windows, <strong>make sure it is the
Miniconda3 installer</strong>, and simply double-click the exe file. For Linux or Mac,
run:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># If Mac</span>
<span class="n">bash</span> <span class="n">Miniconda3</span><span class="o">-</span><span class="n">latest</span><span class="o">-</span><span class="n">MacOSX</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
<span class="c1"># If Linux</span>
<span class="n">bash</span> <span class="n">Miniconda3</span><span class="o">-</span><span class="n">latest</span><span class="o">-</span><span class="n">Linux</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>Note that you may need to create a new terminal after this step in order for
the environmental variables added by conda to be loaded.</p>
</div>
<div class="section" id="step-2b-optional-create-a-conda-environment">
<h2>Step 2b: (Optional) Create a conda environment<a class="headerlink" href="#step-2b-optional-create-a-conda-environment" title="Permalink to this headline">¶</a></h2>
<p>If you are working with many python packages, it is generally recommended you
create a separate environment for each of your packages. For example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">--</span><span class="n">name</span> <span class="n">my_pymatgen</span> <span class="n">python</span>
<span class="n">source</span> <span class="n">activate</span> <span class="n">my_pymatgen</span> <span class="c1"># OSX or Linux</span>
<span class="n">activate</span> <span class="n">my_pymatgen</span> <span class="c1"># Windows</span>
</pre></div>
</div>
</div>
<div class="section" id="step-3-install-pymatgen">
<h2>Step 3: Install pymatgen<a class="headerlink" href="#step-3-install-pymatgen" title="Permalink to this headline">¶</a></h2>
<p>You can install pymatgen via conda as well via the <a class="reference external" href="https://anaconda.org/matsci">matsci channel on
Anaconda cloud</a> maintained by the Materials
Virtual Lab:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">--</span><span class="n">channel</span> <span class="n">matsci</span> <span class="n">pymatgen</span>
</pre></div>
</div>
<p>If the above fails, try using conda to install some critical dependencies and
then do pip install:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">--</span><span class="n">yes</span> <span class="n">numpy</span> <span class="n">scipy</span> <span class="n">matplotlib</span>
<span class="n">pip</span> <span class="n">install</span> <span class="n">pymatgen</span>
</pre></div>
</div>
</div>
<div class="section" id="step-4-optional-install-enumlib-and-bader-only-for-osx-and-linux">
<h2>Step 4: (Optional) Install enumlib and bader (only for OSX and Linux)<a class="headerlink" href="#step-4-optional-install-enumlib-and-bader-only-for-osx-and-linux" title="Permalink to this headline">¶</a></h2>
<p>If you would like to use the enumeration capabilities powered by Gus Hart’s
enumlib or perform Bader charge analysis powered by the Bader analysis code
of the Henkelmann group, the <a class="reference external" href="https://anaconda.org/matsci">matsci channel on Anaconda cloud</a> has builds for enumlib and bader for OSX and
Linux (sorry, Windows users, you are on your own as the develpers of these
packages do not support Windows):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">--</span><span class="n">channel</span> <span class="n">matsci</span> <span class="n">bader</span>
<span class="n">conda</span> <span class="n">install</span> <span class="o">--</span><span class="n">channel</span> <span class="n">matsci</span> <span class="n">enumlib</span>
</pre></div>
</div>
<p>If the above fails, you can also try installing these from source using the pmg
command line tool as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pmg</span> <span class="n">config</span> <span class="o">--</span><span class="n">install</span> <span class="n">enumlib</span>
<span class="n">pmg</span> <span class="n">config</span> <span class="o">--</span><span class="n">install</span> <span class="n">bader</span>
</pre></div>
</div>
<p>Then put these in your PATH somewhere.</p>
</div>
</div>
<div class="section" id="potcar-setup">
<h1>POTCAR Setup<a class="headerlink" href="#potcar-setup" title="Permalink to this headline">¶</a></h1>
<p>For the code to generate POTCAR files, it needs to know where the VASP
pseudopotential files are. We are not allowed to distribute these under the
VASP license. The good news is that the <cite>pmg</cite> command line utility includes a
config functionality.</p>
<p>After installation, do:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pmg</span> <span class="n">config</span> <span class="o">-</span><span class="n">p</span> <span class="o"><</span><span class="n">EXTRACTED_VASP_POTCAR</span><span class="o">></span> <span class="o"><</span><span class="n">MY_PSP</span><span class="o">></span>
</pre></div>
</div>
<p>In the above, <cite><EXTRACTED_VASP_POTCAR></cite> is the location of the directory that
you extracted the downloaded VASP pseudopotential files. Typically, it has
the following format:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-</span> <span class="o"><</span><span class="n">EXTRACTED_VASP_POTCAR</span><span class="o">></span>
<span class="o">|-</span> <span class="n">POT_GGA_PAW_PBE</span>
<span class="o">||-</span> <span class="n">Ac_s</span>
<span class="o">|||-</span><span class="n">POTCAR</span>
<span class="o">|||-...</span>
</pre></div>
</div>
<p>or:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-</span> <span class="o"><</span><span class="n">EXTRACTED_VASP_POTCAR</span><span class="o">></span>
<span class="o">|-</span> <span class="n">potpaw_PBE</span>
<span class="o">||-</span> <span class="n">Ac_s</span>
<span class="o">|||-</span><span class="n">POTCAR</span>
<span class="o">|||-...</span>
</pre></div>
</div>
<p>and follow the instructions. If you have done it correctly, you should get a
resources directory with the following directory structure:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-</span> <span class="n">psp_resources</span>
<span class="o">|-</span> <span class="n">POT_GGA_PAW_PBE</span>
<span class="o">||-</span> <span class="n">POTCAR</span><span class="o">.</span><span class="n">Ac_s</span><span class="o">.</span><span class="n">gz</span>
<span class="o">||-</span> <span class="n">POTCAR</span><span class="o">.</span><span class="n">Ac</span><span class="o">.</span><span class="n">gz</span>
<span class="o">||-</span> <span class="n">POTCAR</span><span class="o">.</span><span class="n">Ag</span><span class="o">.</span><span class="n">gz</span>
<span class="o">...</span>
<span class="o">|-</span> <span class="n">POT_GGA_PAW_PW91</span>
<span class="o">...</span>
</pre></div>
</div>
<p>After generating the resources directory, you should add a VASP_PSP_DIR config
variable pointing to the generated directory and you should then be
able to generate POTCARs:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pmg</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">PMG_VASP_PSP_DIR</span> <span class="o"><</span><span class="n">MY_PSP</span><span class="o">></span>
</pre></div>
</div>
<p>If you are using newer sets of pseudopotential files from VASP, the directory
names may be different, e.g., POT_GGA_PAW_PBE_52. For such cases, please also
add a default functional specification as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pmg</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">PMG_DEFAULT_FUNCTIONAL</span> <span class="n">PBE_52</span>
</pre></div>
</div>
<p>You can also use this to specify whatever functional you would like to use by
default in pymatgen, e.g., LDA_52, PW91, etc. Type:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pmg</span> <span class="n">potcar</span> <span class="o">-</span><span class="n">h</span>
</pre></div>
</div>
<p>to see full list of choices.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The Materials Project uses the 2012 versions of the VASP pseudopotentials.
As such, the pymatgen compatibility package assume this version. If you use
any functional other than PBE, note that you should not be combining results
from these other functionals with Materials Project data.</p>
</div>
</div>
<div class="section" id="setup-for-developers-using-github">
<h1>Setup for Developers (using GitHub)<a class="headerlink" href="#setup-for-developers-using-github" title="Permalink to this headline">¶</a></h1>
<div class="section" id="step-1-preparing-your-system">
<h2>Step 1: Preparing your system<a class="headerlink" href="#step-1-preparing-your-system" title="Permalink to this headline">¶</a></h2>
<div class="section" id="windows">
<h3>Windows<a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h3>
<ol class="arabic simple">
<li><p>Download Microsoft Visual Studio 2015 (the free Community Edition) is fine.</p></li>
<li><p>Install Visual Studio 2015, but <em>make sure that you select More Options ->
Programming Languages -> Visual C++ during the installation process</em>. By
default, Visual Studio does not install Visual C++, which is needed.</p></li>
</ol>
</div>
<div class="section" id="mac-osx">
<h3>Mac OSX<a class="headerlink" href="#mac-osx" title="Permalink to this headline">¶</a></h3>
<ol class="arabic">
<li><p>Download and install Xcode. Afterwards, install the XCode command line
tools by typing the following in a terminal:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">xcode</span><span class="o">-</span><span class="n">select</span> <span class="o">--</span><span class="n">install</span>
</pre></div>
</div>
</li>
<li><p>(Optional) Install gfortran. Get an installer at
<a class="reference external" href="http://gcc.gnu.org/wiki/GFortranBinaries#MacOS">http://gcc.gnu.org/wiki/GFortranBinaries#MacOS</a>.</p></li>
</ol>
</div>
<div class="section" id="linux">
<h3>Linux<a class="headerlink" href="#linux" title="Permalink to this headline">¶</a></h3>
<ol class="arabic simple">
<li><p>Usually no preparation is needed as most of the standard compilers should
already be available.</p></li>
</ol>
</div>
</div>
<div class="section" id="step-2-install-pymatgen-in-developmental-mode">
<h2>Step 2: Install pymatgen in developmental mode<a class="headerlink" href="#step-2-install-pymatgen-in-developmental-mode" title="Permalink to this headline">¶</a></h2>
<ol class="arabic">
<li><p>Make sure you have git and <a class="reference external" href="https://git-lfs.github.com/">git-lfs</a> installed.
Clone the repo at <a class="reference external" href="https://github.com/materialsproject/pymatgen">https://github.com/materialsproject/pymatgen</a>.</p></li>
<li><p>Run <cite>git lfs install</cite> in the cloned repo first.</p></li>
<li><p>In your root pymatgen repo directory, type (you may need to do this with root
privileges):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">e</span> <span class="o">.</span>
</pre></div>
</div>
</li>
<li><p>Install any missing python libraries that are necessary.</p></li>
</ol>
<p>I recommend that you start by reading some of the unittests in the tests
subdirectory for each package. The unittests demonstrate the expected behavior
and functionality of the code.</p>
<p>Please read up on pymatgen’s <a class="reference internal" href="contributing.html"><span class="doc">coding guidelines</span></a> before
you start coding. It will make integration much easier.</p>
</div>
</div>
<div class="section" id="installation-tips-for-optional-libraries">
<h1>Installation tips for optional libraries<a class="headerlink" href="#installation-tips-for-optional-libraries" title="Permalink to this headline">¶</a></h1>
<p>This section provides a guide for installing various optional libraries used in
pymatgen. Some of the python libraries are rather tricky to build in certain
operating systems, especially for users unfamiliar with building C/C++ code.
Please feel free to send in suggestions to update the instructions based on
your experiences. In all the instructions, it is assumed that you have standard
gcc and other compilers (e.g., Xcode on Macs) already installed.</p>
<div class="section" id="vtk-on-mac-os-x-tested-on-v7-0">
<h2>VTK on Mac OS X (tested on v7.0)<a class="headerlink" href="#vtk-on-mac-os-x-tested-on-v7-0" title="Permalink to this headline">¶</a></h2>
<p>The easiest is to install cmake from
<a class="reference external" href="http://cmake.org/cmake/resources/software.html">http://cmake.org/cmake/resources/software.html</a>.</p>
<p>Type the following:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">VTK</span> <span class="p">(</span><span class="n">this</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">directory</span> <span class="n">you</span> <span class="n">expanded</span> <span class="n">VTK</span> <span class="n">into</span><span class="p">)</span>
<span class="n">mkdir</span> <span class="n">build</span>
<span class="n">cd</span> <span class="n">build</span>
<span class="n">ccmake</span> <span class="o">..</span> <span class="p">(</span><span class="n">this</span> <span class="n">uses</span> <span class="n">cmake</span> <span class="ow">in</span> <span class="n">an</span> <span class="n">interactive</span> <span class="n">manner</span><span class="p">)</span>
</pre></div>
</div>
<p>Press “t” to toggle advanced mode. Then press “c” to do an initial
configuration. After the list of parameters come out, ensure that the
PYTHON_VERSION is set to 3, the VTK_WRAP_PYTHON is set to ON, and
BUILD_SHARED_LIBS is set to ON. You may also need to modify the python
paths and library paths if they are in non-standard locations. For example, if
you have installed the official version of Python instead of using the
Mac-provided version, you will probably need to edit the CMakeCache Python
links. Example configuration for Python 3.5 installed using conda is given
below (only variables that need to be modified/checked are shown):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">PYTHON_EXECUTABLE</span><span class="p">:</span><span class="n">FILEPATH</span><span class="o">=/</span><span class="n">Users</span><span class="o">/<</span><span class="n">username</span><span class="o">>/</span><span class="n">miniconda3</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">python3</span>
<span class="n">PYTHON_INCLUDE_DIR</span><span class="p">:</span><span class="n">PATH</span><span class="o">=/</span><span class="n">Users</span><span class="o">/<</span><span class="n">username</span><span class="o">>/</span><span class="n">miniconda3</span><span class="o">/</span><span class="n">include</span><span class="o">/</span><span class="n">python3</span><span class="o">.</span><span class="mi">5</span><span class="n">m</span>
<span class="n">PYTHON_LIBRARY</span><span class="p">:</span><span class="n">FILEPATH</span><span class="o">=/</span><span class="n">Users</span><span class="o">/<</span><span class="n">username</span><span class="o">>/</span><span class="n">miniconda3</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">libpython3</span><span class="o">.</span><span class="mi">5</span><span class="n">m</span><span class="o">.</span><span class="n">dylib</span>
<span class="n">VTK_INSTALL_PYTHON_MODULE_DIR</span><span class="p">:</span><span class="n">PATH</span><span class="o">=/</span><span class="n">Users</span><span class="o">/<</span><span class="n">username</span><span class="o">>/</span><span class="n">miniconda3</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">python3</span><span class="o">.</span><span class="mi">5</span><span class="o">/</span><span class="n">site</span><span class="o">-</span><span class="n">packages</span>
<span class="n">VTK_PYTHON_VERSION</span><span class="p">:</span><span class="n">STRING</span><span class="o">=</span><span class="mi">3</span>
<span class="n">VTK_WRAP_PYTHON</span><span class="p">:</span><span class="n">BOOL</span><span class="o">=</span><span class="n">ON</span>
</pre></div>
</div>
<p>Then press “c” again to configure and finally “g” to generate the required
make files After the CMakeCache.txt file is generated, type:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="o">-</span><span class="n">j</span> <span class="mi">4</span>
<span class="n">sudo</span> <span class="n">make</span> <span class="n">install</span>
</pre></div>
</div>
<p>With any luck, you should have vtk with the necessary python wrappers
installed. You can test this by going into a python terminal and trying:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">vtk</span>
</pre></div>
</div>
</div>
<div class="section" id="openbabel-mac-os-x-tested-on-v2-3-2">
<h2>OpenBabel Mac OS X (tested on v2.3.2)<a class="headerlink" href="#openbabel-mac-os-x-tested-on-v2-3-2" title="Permalink to this headline">¶</a></h2>
<p><strong>Anaconda install</strong></p>
<p>If you are using anaconda (and have pymatgen installed in your anaconda environment), you should be
able to install openbabel with a single command:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">openbabel</span> <span class="n">openbabel</span>
</pre></div>
</div>
<p><strong>Manual install</strong></p>
<p>Openbabel must be compiled with python bindings for integration with pymatgen.
Here are the steps that I took to make it work:</p>
<ol class="arabic">
<li><p>Install cmake from <a class="reference external" href="http://cmake.org/cmake/resources/software.html">http://cmake.org/cmake/resources/software.html</a>.</p></li>
<li><p>Install pcre-8.33 from
<a class="reference external" href="ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.33.tar.gz">ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.33.tar.gz</a>.</p></li>
<li><p>Install pkg-config-0.28 using MacPorts or from
<a class="reference external" href="http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz">http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz</a>.</p></li>
<li><p>Install SWIG from
<a class="reference external" href="http://prdownloads.sourceforge.net/swig/swig-2.0.10.tar.gz">http://prdownloads.sourceforge.net/swig/swig-2.0.10.tar.gz</a>.</p></li>
<li><p>Download openbabel 2.3.2 <em>source code</em> from
<a class="reference external" href="https://sourceforge.net/projects/openbabel/files/openbabel/2.3.2/">https://sourceforge.net/projects/openbabel/files/openbabel/2.3.2/</a>.</p></li>
<li><p>Download Eigen version 3.1.2 from
<a class="reference external" href="http://bitbucket.org/eigen/eigen/get/3.1.2.tar.gz">http://bitbucket.org/eigen/eigen/get/3.1.2.tar.gz</a>.</p></li>
<li><p>Extract your Eigen and openbabel source distributions:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tar</span> <span class="o">-</span><span class="n">zxvf</span> <span class="n">openbabel</span><span class="o">-</span><span class="mf">2.3</span><span class="o">.</span><span class="mf">2.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
<span class="n">tar</span> <span class="o">-</span><span class="n">zxvf</span> <span class="n">eigen3</span><span class="o">.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
</pre></div>
</div>
</li>
<li><p>Now you should have two directories. Assuming that your openbabel src is in
a directory called “openbabel-2.3.2” and your eigen source is in a directory
called “eigen3”, do the following steps:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mv</span> <span class="n">openbabel</span><span class="o">-</span><span class="mf">2.3</span><span class="o">.</span><span class="mi">2</span> <span class="n">ob</span><span class="o">-</span><span class="n">src</span>
<span class="n">cd</span> <span class="n">ob</span><span class="o">-</span><span class="n">src</span><span class="o">/</span><span class="n">scripts</span><span class="o">/</span><span class="n">python</span><span class="p">;</span> <span class="n">rm</span> <span class="n">openbabel</span><span class="o">.</span><span class="n">py</span> <span class="n">openbabel</span><span class="o">-</span><span class="n">python</span><span class="o">.</span><span class="n">cpp</span><span class="p">;</span> <span class="n">cd</span> <span class="o">../../..</span>
</pre></div>
</div>
</li>
<li><p>Edit ob-src/scripts/CMakeLists.txt, jump to line 70, change “eigen2_define”
to “eigen_define”.</p></li>
<li><p>Let’s create a build directory:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="n">ob</span><span class="o">-</span><span class="n">build</span>
<span class="n">cd</span> <span class="n">ob</span><span class="o">-</span><span class="n">build</span>
<span class="n">cmake</span> <span class="o">-</span><span class="n">DPYTHON_BINDINGS</span><span class="o">=</span><span class="n">ON</span> <span class="o">-</span><span class="n">DRUN_SWIG</span><span class="o">=</span><span class="n">ON</span> <span class="o">-</span><span class="n">DEIGEN3_INCLUDE_DIR</span><span class="o">=../</span><span class="n">eigen3</span> <span class="o">../</span><span class="n">ob</span><span class="o">-</span><span class="n">src</span> <span class="mi">2</span><span class="o">>&</span><span class="mi">1</span> <span class="o">|</span> <span class="n">tee</span> <span class="n">cmake</span><span class="o">.</span><span class="n">out</span>
</pre></div>
</div>
</li>
<li><p>Before proceeding further, similar to the VTK installation process in the
previous section, you may also need to modify the CMakeCache.txt
file by hand if your python paths and library paths if they are in
non-standard locations. For example, if you have installed the official
version of Python instead of using the Mac-provided version,
you will probably need to edit the CMakeCache Python links. Example
configuration for Python 2.7 is given below (only variables that need to
be modified are shown):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">//</span><span class="n">Path</span> <span class="n">to</span> <span class="n">a</span> <span class="n">program</span><span class="o">.</span>
<span class="n">PYTHON_EXECUTABLE</span><span class="p">:</span><span class="n">FILEPATH</span><span class="o">=/</span><span class="n">Library</span><span class="o">/</span><span class="n">Frameworks</span><span class="o">/</span><span class="n">Python</span><span class="o">.</span><span class="n">framework</span><span class="o">/</span><span class="n">Versions</span><span class="o">/</span><span class="mf">2.7</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">python</span>
<span class="o">//</span><span class="n">Path</span> <span class="n">to</span> <span class="n">a</span> <span class="n">file</span><span class="o">.</span>
<span class="n">PYTHON_INCLUDE_DIR</span><span class="p">:</span><span class="n">PATH</span><span class="o">=/</span><span class="n">Library</span><span class="o">/</span><span class="n">Frameworks</span><span class="o">/</span><span class="n">Python</span><span class="o">.</span><span class="n">framework</span><span class="o">/</span><span class="n">Versions</span><span class="o">/</span><span class="mf">2.7</span><span class="o">/</span><span class="n">Headers</span>
<span class="o">//</span><span class="n">Path</span> <span class="n">to</span> <span class="n">a</span> <span class="n">library</span><span class="o">.</span>
<span class="n">PYTHON_LIBRARY</span><span class="p">:</span><span class="n">FILEPATH</span><span class="o">=/</span><span class="n">Library</span><span class="o">/</span><span class="n">Frameworks</span><span class="o">/</span><span class="n">Python</span><span class="o">.</span><span class="n">framework</span><span class="o">/</span><span class="n">Versions</span><span class="o">/</span><span class="mf">2.7</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">libpython2</span><span class="o">.</span><span class="mf">7.</span><span class="n">dylib</span>
</pre></div>
</div>
</li>
<li><p>If you are using Mavericks (OSX 10.9) and encounter errors relating to <tr1/memory>, you might also need to include
the following flag in your CMakeCache.txt:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">CMAKE_CXX_FLAGS</span><span class="p">:</span><span class="n">STRING</span><span class="o">=-</span><span class="n">stdlib</span><span class="o">=</span><span class="n">libstdc</span><span class="o">++</span>
</pre></div>
</div>
</li>
<li><p>Run make and install as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="o">-</span><span class="n">j2</span>
<span class="n">sudo</span> <span class="n">make</span> <span class="n">install</span>
</pre></div>
</div>
</li>
<li><p>With any luck, you should have openbabel with python bindings installed.
You can test your installation by trying to import openbabel from the
python command line. Please note that despite best efforts,
openbabel seems to install the python bindings into /usr/local/lib even
if your Python is not the standard Mac version. In that case,
you may need to add the following into your .bash_profile:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export PYTHONPATH=/usr/local/lib:$PYTHONPATH
</pre></div>
</div>
</li>
</ol>
</div>
<div class="section" id="zeo">
<h2>Zeo++<a class="headerlink" href="#zeo" title="Permalink to this headline">¶</a></h2>
<p>If you use the defects analysis package, you will need to installZeo++/Voro++.
Here are the steps you need to follow (thanks to Bharat)</p>
<p>Download and install Voro++:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="n">Voro</span><span class="o">++</span>
<span class="n">mkdir</span> <span class="n">Voro</span><span class="o">++/</span><span class="n">voro</span>
<span class="n">cd</span> <span class="n">Voro</span><span class="o">++/</span><span class="n">voro</span>
<span class="n">svn</span> <span class="n">checkout</span> <span class="o">--</span><span class="n">username</span> <span class="n">anonsvn</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">code</span><span class="o">.</span><span class="n">lbl</span><span class="o">.</span><span class="n">gov</span><span class="o">/</span><span class="n">svn</span><span class="o">/</span><span class="n">voro</span><span class="o">/</span><span class="n">trunk</span> <span class="c1"># password is 'anonsvn'</span>
<span class="n">cd</span> <span class="n">trunk</span>
</pre></div>
</div>
<p>Add -fPIC to the CFLAGS variable in config.mk, and then:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">make</span>
</pre></div>
</div>
<p>Download and install Zeo++:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="n">Zeo</span><span class="o">++</span>
<span class="n">mkdir</span> <span class="n">Zeo</span><span class="o">++/</span><span class="n">zeo</span>
<span class="n">cd</span> <span class="n">Zeo</span><span class="o">++/</span><span class="n">zeo</span>
<span class="n">svn</span> <span class="n">checkout</span> <span class="o">--</span><span class="n">username</span> <span class="n">anonsvn</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">code</span><span class="o">.</span><span class="n">lbl</span><span class="o">.</span><span class="n">gov</span><span class="o">/</span><span class="n">svn</span><span class="o">/</span><span class="n">zeo</span><span class="o">/</span><span class="n">trunk</span> <span class="c1"># password is 'anonsvn'</span>
<span class="n">cd</span> <span class="n">trunk</span>
<span class="n">make</span> <span class="n">dylib</span>
</pre></div>
</div>
<p>Create python bindings with Cython:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">cython</span>
<span class="n">cd</span> <span class="n">cython_wrapper</span>
<span class="n">python</span> <span class="n">setup_alt</span><span class="o">.</span><span class="n">py</span> <span class="n">develop</span>
</pre></div>
</div>
<p>To test that the installation worked, here is an example series of things you
can do using pymatgen:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">In</span> <span class="p">[</span><span class="mi">1</span><span class="p">]:</span> <span class="kn">from</span> <span class="nn">pymatgen.analysis.defects.point_defects</span> <span class="k">import</span> <span class="n">Interstitial</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">2</span><span class="p">]:</span> <span class="kn">from</span> <span class="nn">pymatgen.core.structure</span> <span class="k">import</span> <span class="n">Structure</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">3</span><span class="p">]:</span> <span class="n">structure</span> <span class="o">=</span> <span class="n">Structure</span><span class="o">.</span><span class="n">from_file</span><span class="p">(</span><span class="s1">'/path/to/file'</span><span class="p">)</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">4</span><span class="p">]:</span> <span class="n">radii</span><span class="p">,</span> <span class="n">valences</span> <span class="o">=</span> <span class="p">{},</span> <span class="p">{}</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">5</span><span class="p">]:</span> <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">structure</span><span class="o">.</span><span class="n">composition</span><span class="o">.</span><span class="n">elements</span><span class="p">:</span>
<span class="o">...</span><span class="p">:</span> <span class="n">radii</span><span class="p">[</span><span class="n">element</span><span class="o">.</span><span class="n">symbol</span><span class="p">]</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">atomic_radius</span>
<span class="o">...</span><span class="p">:</span> <span class="n">valence</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">group</span> <span class="c1"># Just a first guess..</span>
<span class="o">...</span><span class="p">:</span> <span class="k">if</span> <span class="n">element</span><span class="o">.</span><span class="n">group</span> <span class="o">></span> <span class="mi">12</span><span class="p">:</span>
<span class="o">...</span><span class="p">:</span> <span class="n">valence</span> <span class="o">-=</span> <span class="mi">10</span>
<span class="o">...</span><span class="p">:</span> <span class="n">valences</span><span class="p">[</span><span class="n">element</span><span class="o">.</span><span class="n">symbol</span><span class="p">]</span> <span class="o">=</span> <span class="n">valence</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">6</span><span class="p">]:</span> <span class="n">interstitial</span> <span class="o">=</span> <span class="n">Interstitial</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="n">radii</span><span class="o">=</span><span class="n">radii</span><span class="p">,</span> <span class="n">valences</span><span class="o">=</span><span class="n">valences</span><span class="p">)</span>
<span class="n">In</span> <span class="p">[</span><span class="mi">7</span><span class="p">]:</span> <span class="n">interstitial</span><span class="o">.</span><span class="n">_defect_sites</span>
</pre></div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h3><a href="index.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Requirements</a><ul>
<li><a class="reference internal" href="#optional-dependencies">Optional dependencies</a></li>
<li><a class="reference internal" href="#optional-non-python-programs">Optional non-Python programs</a></li>
</ul>
</li>
<li><a class="reference internal" href="#conda-based-install">Conda-based install</a><ul>
<li><a class="reference internal" href="#step-1-install-conda">Step 1: Install conda</a></li>
<li><a class="reference internal" href="#step-2b-optional-create-a-conda-environment">Step 2b: (Optional) Create a conda environment</a></li>
<li><a class="reference internal" href="#step-3-install-pymatgen">Step 3: Install pymatgen</a></li>
<li><a class="reference internal" href="#step-4-optional-install-enumlib-and-bader-only-for-osx-and-linux">Step 4: (Optional) Install enumlib and bader (only for OSX and Linux)</a></li>
</ul>
</li>
<li><a class="reference internal" href="#potcar-setup">POTCAR Setup</a></li>
<li><a class="reference internal" href="#setup-for-developers-using-github">Setup for Developers (using GitHub)</a><ul>
<li><a class="reference internal" href="#step-1-preparing-your-system">Step 1: Preparing your system</a><ul>
<li><a class="reference internal" href="#windows">Windows</a></li>
<li><a class="reference internal" href="#mac-osx">Mac OSX</a></li>
<li><a class="reference internal" href="#linux">Linux</a></li>
</ul>
</li>
<li><a class="reference internal" href="#step-2-install-pymatgen-in-developmental-mode">Step 2: Install pymatgen in developmental mode</a></li>
</ul>
</li>
<li><a class="reference internal" href="#installation-tips-for-optional-libraries">Installation tips for optional libraries</a><ul>
<li><a class="reference internal" href="#vtk-on-mac-os-x-tested-on-v7-0">VTK on Mac OS X (tested on v7.0)</a></li>
<li><a class="reference internal" href="#openbabel-mac-os-x-tested-on-v2-3-2">OpenBabel Mac OS X (tested on v2.3.2)</a></li>
<li><a class="reference internal" href="#zeo">Zeo++</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="index.html"
title="previous chapter">Introduction</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="usage.html"
title="next chapter">Overview</a></p>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/installation.rst.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
<a href="usage.html" title="Overview"
>next</a> |</li>
<li class="right" >
<a href="index.html" title="Introduction"
>previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">pymatgen 2019.5.1 documentation</a> »</li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2011, Pymatgen Development Team.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.0.1.
</div>
<div class="footer">This page uses <a href="http://analytics.google.com/">
Google Analytics</a> to collect statistics. You can disable it by blocking
the JavaScript coming from www.google-analytics.com.
<script type="text/javascript">
(function() {
var ga = document.createElement('script');
ga.src = ('https:' == document.location.protocol ?
'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
ga.setAttribute('async', 'true');
document.documentElement.firstChild.appendChild(ga);
})();
</script>
</div>
</body>
</html>