/usr/share/doc/psi4/html/external.html is in psi4-data 1:0.3-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Installation and Runtime Configuration — Psi4 [] Docs</title>
<link rel="stylesheet" href="_static/psi4.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="./" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</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/jquery.cookie.js"></script>
<script type="text/javascript" src="_static/toggle_sections.js"></script>
<script type="text/javascript" src="_static/toggle_sidebar.js"></script>
<script type="text/javascript" src="_static/toggle_codeprompt.js"></script>
<link rel="shortcut icon" href="_static/favicon-psi4.ico"/>
<link rel="top" title="Psi4 [] Docs" href="index.html" />
<link rel="next" title="Binary Distribution" href="conda.html" />
<link rel="prev" title="<no title>" href="cfour_table_grad.html" />
</head>
<body role="document">
<div class="relbar-top">
<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="contents.html" title="Table Of Contents"
accesskey="C">toc</a> </li>
<li class="right" >
<a href="conda.html" title="Binary Distribution"
accesskey="N">next</a> </li>
<li class="right" >
<a href="cfour_table_grad.html" title="<no title>"
accesskey="P">previous</a> </li>
<li><a href="index.html">Psi4 []</a> » </li>
</ul>
</div>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<a class="reference internal image-reference" href="_images/psi4banner.png"><img alt="Psi4 Project Logo" src="_images/psi4banner.png" style="width: 100%;" /></a>
<div class="section" id="installation-and-runtime-configuration">
<h1>Installation and Runtime Configuration<a class="headerlink" href="#installation-and-runtime-configuration" title="Permalink to this headline">¶</a></h1>
<div class="section" id="obtaining-psifour">
<h2>Obtaining <span class="sc">Psi4</span><a class="headerlink" href="#obtaining-psifour" title="Permalink to this headline">¶</a></h2>
<p>The latest version of the <span class="sc">Psi4</span> program package may be
obtained at <a class="reference external" href="http://www.psicode.org">www.psicode.org</a>. The
package is available as a binary for Linux (<a class="reference internal" href="conda.html#sec-conda"><span>Installing
from Binary</span></a>) or as source code (zipped
archive or git repository from <a class="reference external" href="http://www.github.com/psi4/psi4public">www.github.com/psi4/psi4public</a>).</p>
</div>
<div class="section" id="installing-from-binary">
<h2>Installing from Binary<a class="headerlink" href="#installing-from-binary" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="conda.html">Binary Distribution</a><ul>
<li class="toctree-l2"><a class="reference internal" href="conda.html#quick-installation">Quick Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="conda.html#detailed-installation-of-miniconda">Detailed Installation of Miniconda</a></li>
<li class="toctree-l2"><a class="reference internal" href="conda.html#detailed-installation-of-psifour">Detailed Installation of <span class="sc">Psi4</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="conda.html#useful-commands">Useful Commands</a></li>
<li class="toctree-l2"><a class="reference internal" href="conda.html#troubleshooting">Troubleshooting</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="compiling-and-installing-from-source">
<span id="sec-installfile"></span><span id="index-0"></span><h2>Compiling and Installing from Source<a class="headerlink" href="#compiling-and-installing-from-source" title="Permalink to this headline">¶</a></h2>
<p>Detailed directions on
<a class="reference external" href="https://github.com/psi4/psi4public/wiki/1_Obtaining">obtaining</a>,
<a class="reference external" href="https://github.com/psi4/psi4public/wiki/2_Planning#-what-are-the-tools-and-dependencies-strictly-required-for-building-psi4">prerequisites</a>,
<a class="reference external" href="https://github.com/psi4/psi4public/wiki/3_Building">building and installing</a>,
and <a class="reference external" href="https://github.com/psi4/psi4public/wiki/0_FAQ">FAQ</a>
are maintained on the <a class="reference external" href="https://github.com/psi4/psi4public/wiki">GitHub Wiki</a>.
If uncertain, <a class="reference external" href="https://github.com/psi4/psi4public/wiki/1_Obtaining#quiz">start here</a>.</p>
</div>
<div class="section" id="scratch-files-and-the-psirc-file">
<span id="sec-psirc"></span><span id="index-1"></span><h2>Scratch Files and the <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> File<a class="headerlink" href="#scratch-files-and-the-psirc-file" title="Permalink to this headline">¶</a></h2>
<p>One very important part of user configuration at the end of the
installation process (<a class="reference internal" href="installfile.html#sec-install-iii-7"><span>details here</span></a>)
is to tell <span class="sc">Psi4</span> where to write its temporary
(“scratch”) files. Electronic structure packages like <span class="sc">Psi4</span> can
create rather large temporary disk files. It is very important to
ensure that <span class="sc">Psi4</span> is writing its temporary files to a disk drive
phsyically attached to the computer running the computation. If it
is not, it will significantly slow down the program and the network.
By default, <span class="sc">Psi4</span> will write temporary files to <code class="docutils literal"><span class="pre">/tmp</span></code>, but this
directory is often not large enough for typical computations. Therefore,
you need to (a) make sure there is a sufficiently large directory on a
locally attached disk drive (100GB–1TB or more, depending on the size of
the molecules to be studied) and (b) tell <span class="sc">Psi4</span> the path to this
directory. Scratch file location can be specified through the
<span class="target" id="index-2"></span><a class="reference internal" href="#envvar-PSI_SCRATCH"><code class="xref std std-envvar docutils literal"><span class="pre">PSI_SCRATCH</span></code></a> environment variable or, more flexibly, through
a resource file, <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> (example <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/example_psi4rc_file">psi4/samples/example_psi4rc_file</a>).</p>
<p>For convenience, the Python interpreter will execute the contents of the
<code class="docutils literal"><span class="pre">~/.psi4rc</span></code> file in the current user’s home area (if present) before performing any
tasks in the input file. The primary use of the <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> file is to control the
handling of scratch files. <span class="sc">Psi4</span> has a number of utilities that manage
input and output (I/O) of quantities to and from the hard disk. Most
quantities, such as molecular integrals, are intermediates that are not of
interest to the user and can be deleted after the computation finishes, but
pertinent details of computations are also written to a checkpoint file and
might be useful in subsequent computations. All files are written to the
designated scratch numbered by <a class="reference internal" href="autodoc_psifiles.html#apdx-psifiles"><span>content</span></a> and labeled
with the process id, then are deleted at the end of the computation,
unless otherwise instructed by the user.</p>
<p>A Python callable handle to the <span class="sc">Psi4</span> I/O management routines is available,
and is called <code class="docutils literal"><span class="pre">psi4_io</span></code>. To instruct the I/O manager to send all files to
another location, say <code class="docutils literal"><span class="pre">/scratch/user</span></code>, add the following command to the <code class="docutils literal"><span class="pre">~/.psi4rc</span></code>
file.:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">psi4_io</span><span class="o">.</span><span class="n">set_default_path</span><span class="p">(</span><span class="s">'/scratch/user'</span><span class="p">)</span>
</pre></div>
</div>
<p>For batch jobs running through a queue, it might be more convenient to use an
environmental variable (in this case <code class="docutils literal"><span class="pre">$MYSCRATCH</span></code>) to set the scratch directory;
the following code will do that:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">os</span>
<span class="n">scratch_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'MYSCRATCH'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">scratch_dir</span><span class="p">:</span>
<span class="n">psi4_io</span><span class="o">.</span><span class="n">set_default_path</span><span class="p">(</span><span class="n">scratch_dir</span> <span class="o">+</span> <span class="s">'/'</span><span class="p">)</span>
</pre></div>
</div>
<p>Individual files can be sent to specific locations. For example, file 32 is
the checkpoint file that the user might want to retain in the working directory
(<em>i.e.</em>, where <span class="sc">Psi4</span> was launched from) for restart purposes. This is
accomplished by the commands below:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">psi4_io</span><span class="o">.</span><span class="n">set_specific_path</span><span class="p">(</span><span class="mi">32</span><span class="p">,</span> <span class="s">'./'</span><span class="p">)</span>
<span class="n">psi4_io</span><span class="o">.</span><span class="n">set_specific_retention</span><span class="p">(</span><span class="mi">32</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
</pre></div>
</div>
<p>which is equivalent to</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">psi4_io</span><span class="o">.</span><span class="n">set_specific_path</span><span class="p">(</span><span class="n">PSIF_CHKPT</span><span class="p">,</span> <span class="s">'./'</span><span class="p">)</span>
<span class="n">psi4_io</span><span class="o">.</span><span class="n">set_specific_retention</span><span class="p">(</span><span class="n">PSIF_CHKPT</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
</pre></div>
</div>
<p>A guide to the contents of individual scratch files may be found at <a class="reference internal" href="autodoc_psifiles.html#apdx-psifiles"><span>PSIOH Intermediate Files</span></a>.
To circumvent difficulties with running multiple jobs in the same scratch, the
process ID (PID) of the <span class="sc">Psi4</span> instance is incorporated into the full file
name; therefore, it is safe to use the same scratch directory for calculations
running simultaneously.</p>
<p>To override any of these defaults for selected jobs, simply place the
appropriate commands from the snippets above in the input file itself. During
excecution, the <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> defaults will be loaded in first, but then the commands
in the input file will be executed. Executing <span class="sc">Psi4</span> with the <a class="reference internal" href="#cmdoption-psi4-m"><code class="xref std std-option docutils literal"><span class="pre">psi4</span> <span class="pre">-m</span></code></a> (for
messy) flag will prevent files being deleted at the end of the run:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">psi4</span> <span class="o">-</span><span class="n">m</span>
</pre></div>
</div>
<p>Alternately, the scratch directory can be set through the environment
variable <span class="target" id="index-3"></span><a class="reference internal" href="#envvar-PSI_SCRATCH"><code class="xref std std-envvar docutils literal"><span class="pre">PSI_SCRATCH</span></code></a> (overrides <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> settings). (First line
for C shell; second line for bash.)</p>
<div class="highlight-python"><div class="highlight"><pre>setenv PSI_SCRATCH /scratch/user
export PSI_SCRATCH=/scratch/user
</pre></div>
</div>
<p>The <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> file can also be used to define constants that are accessible
in input files or to place any Python statements that should be executed
with every <span class="sc">Psi4</span> instance.</p>
</div>
<div class="section" id="threading">
<span id="sec-threading"></span><span id="index-4"></span><h2>Threading<a class="headerlink" href="#threading" title="Permalink to this headline">¶</a></h2>
<p>Most new modules in <span class="sc">Psi4</span> are designed to run efficiently on SMP architectures
via application of several thread models. The de facto standard for <span class="sc">Psi4</span>
involves using threaded BLAS/LAPACK (particularly Intel’s excellent MKL package)
for most tensor-like operations, OpenMP for more general operations, and Boost
Threads for some special-case operations. Note: Using OpenMP alone is a really
bad idea. The developers make little to no effort to explicitly parallelize
operations which are already easily threaded by MKL or other threaded BLAS. Less
than 20% of the threaded code in <span class="sc">Psi4</span> uses OpenMP, the rest is handled by
parallel DGEMM and other library routines. From this point forward, it is
assumed that you have compiled <span class="sc">Psi4</span> with OpenMP and MKL (Note that it is
possible to use g++ or another compiler and yet still link against MKL).</p>
<p>Control of threading in <span class="sc">Psi4</span> can be accomplished at a variety of levels,
ranging from global environment variables to direct control of thread count in
the input file, to even directives specific to each model. This hierarchy is
explained below. Note that each deeper level trumps all previous levels.</p>
<p class="rubric">(1) OpenMP/MKL Environment Variables</p>
<p>The easiest/least visible way to thread <span class="sc">Psi4</span> is to set the standard OpenMP/MKL
environment variables <span class="target" id="index-5"></span><a class="reference internal" href="#envvar-OMP_NUM_THREADS"><code class="xref std std-envvar docutils literal"><span class="pre">OMP_NUM_THREADS</span></code></a> and <span class="target" id="index-6"></span><a class="reference internal" href="#envvar-MKL_NUM_THREADS"><code class="xref std std-envvar docutils literal"><span class="pre">MKL_NUM_THREADS</span></code></a>.
For instance, in tcsh:</p>
<div class="highlight-python"><div class="highlight"><pre>setenv OMP_NUM_THREADS 4
setenv MKL_NUM_THREADS 4
</pre></div>
</div>
<p><span class="sc">Psi4</span> then detects these value via the API routines in <code class="docutils literal"><span class="pre"><omp.h></span></code> and
<code class="docutils literal"><span class="pre"><mkl.h></span></code>, and runs all applicable code with 4 threads. These environment
variables are typically defined in a <code class="docutils literal"><span class="pre">.tcshrc</span></code> or <code class="docutils literal"><span class="pre">.bashrc</span></code>.</p>
<p class="rubric">(2) The -n Command Line Flag</p>
<p>To change the number of threads at runtime, the <a class="reference internal" href="#cmdoption-psi4-n"><code class="xref std std-option docutils literal"><span class="pre">psi4</span> <span class="pre">-n</span></code></a> flag may be used. An
example is:</p>
<div class="highlight-python"><div class="highlight"><pre>psi4 -i input.dat -o output.dat -n 4
</pre></div>
</div>
<p>which will run on four threads.</p>
<p class="rubric">(3) Setting Thread Numbers in an Input</p>
<p>For more explicit control, the Process::environment class in <span class="sc">Psi4</span> can
override the number of threads set by environment variables. This functionality
is accessed via the <code class="xref py py-func docutils literal"><span class="pre">set_num_threads()</span></code> Psithon function, which controls
both MKL and OpenMP thread numbers. The number of threads may be changed
multiple times in a <span class="sc">Psi4</span> input file. An example input for this feature is:</p>
<div class="highlight-python"><div class="highlight"><pre># A bit small-ish, but you get the idea
molecule h2o {
0 1
O
H 1 1.0
H 1 1.0 2 90.0
}
set scf {
basis cc-pvdz
scf_type df
}
# Run from 1 to 4 threads, for instance, to record timings
for nthread in range(1,5):
set_num_threads(nthread)
energy('scf')
</pre></div>
</div>
<p class="rubric">(4) Method-Specific Control</p>
<p>Even more control is possible in certain circumstances. For instance, the
threaded generation of AO density-fitted integrals involves a memory requirement
proportional to the number of threads. This requirement may exceed the total
memory of a small-memory node if all threads are involved in the generation of
these integrals. For general DF algorithms, the user may specify:</p>
<div class="highlight-python"><div class="highlight"><pre>set MODULE_NAME df_ints_num_threads n
</pre></div>
</div>
<p>to explicitly control the number of threads used for integral formation. Setting
this variable to 0 (the default) uses the number of threads specified by the
<code class="xref py py-func docutils literal"><span class="pre">set_num_threads()</span></code> Psithon method or the default environmental variables.</p>
</div>
<div class="section" id="command-line-options">
<span id="sec-commandlineoptions"></span><h2>Command Line Options<a class="headerlink" href="#command-line-options" title="Permalink to this headline">¶</a></h2>
<p><span class="sc">Psi4</span> can be invoked with no command line arguments, as it takes as input
by default the file “input.dat” and directs output by default to “output.dat”.
The set of three commands below are completely equivalent, while the fourth is,
perhaps, the most common usage.</p>
<div class="highlight-python"><div class="highlight"><pre>psi4
psi4 -i input.dat -o output.dat
psi4 input.dat output.dat
psi4 descriptive_filename.in descriptive_filename.out
</pre></div>
</div>
<p>Command-line arguments to <span class="sc">Psi4</span> can be accessed through <a class="reference internal" href="#cmdoption-psi4--help"><code class="xref std std-option docutils literal"><span class="pre">psi4</span> <span class="pre">--help</span></code></a>.</p>
<dl class="option">
<dt id="cmdoption-psi4-a">
<span id="cmdoption-psi4--append"></span><code class="descname">-a</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--append</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-a" title="Permalink to this definition">¶</a></dt>
<dd><p>Append results to output file. Default: Truncate first</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-d">
<span id="cmdoption-psi4--debug"></span><code class="descname">-d</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--debug</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-d" title="Permalink to this definition">¶</a></dt>
<dd><p>Flush the outfile at every fprintf. Default: true iff <code class="docutils literal"><span class="pre">--with-debug</span></code></p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-h">
<span id="cmdoption-psi4--help"></span><code class="descname">-h</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--help</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-h" title="Permalink to this definition">¶</a></dt>
<dd><p>Display the command-line options and usage information.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-i">
<span id="cmdoption-psi4--input"></span><code class="descname">-i</code><code class="descclassname"> <filename></code><code class="descclassname">, </code><code class="descname">--input</code><code class="descclassname"> <filename></code><a class="headerlink" href="#cmdoption-psi4-i" title="Permalink to this definition">¶</a></dt>
<dd><p>Input file name. Default: input.dat</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-l">
<span id="cmdoption-psi4--psidatadir"></span><code class="descname">-l</code><code class="descclassname"> <name></code><code class="descclassname">, </code><code class="descname">--psidatadir</code><code class="descclassname"> <name></code><a class="headerlink" href="#cmdoption-psi4-l" title="Permalink to this definition">¶</a></dt>
<dd><p>Mainly for use by developers, this overrides the value of
<span class="target" id="index-7"></span><a class="reference internal" href="#envvar-PSIDATADIR"><code class="xref std std-envvar docutils literal"><span class="pre">PSIDATADIR</span></code></a> and specifies the path to the Psi data
library (psi4/lib)</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-m">
<span id="cmdoption-psi4--messy"></span><code class="descname">-m</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--messy</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-m" title="Permalink to this definition">¶</a></dt>
<dd><p>Leave temporary files after the run is completed.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-n">
<span id="cmdoption-psi4--nthread"></span><code class="descname">-n</code><code class="descclassname"> <threads></code><code class="descclassname">, </code><code class="descname">--nthread</code><code class="descclassname"> <threads></code><a class="headerlink" href="#cmdoption-psi4-n" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of threads to use (overrides <span class="target" id="index-8"></span><a class="reference internal" href="#envvar-OMP_NUM_THREADS"><code class="xref std std-envvar docutils literal"><span class="pre">OMP_NUM_THREADS</span></code></a>)</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-o">
<span id="cmdoption-psi4--output"></span><code class="descname">-o</code><code class="descclassname"> <filename></code><code class="descclassname">, </code><code class="descname">--output</code><code class="descclassname"> <filename></code><a class="headerlink" href="#cmdoption-psi4-o" title="Permalink to this definition">¶</a></dt>
<dd><p>Output file name. Use <code class="docutils literal"><span class="pre">stdout</span></code> as <filename> to redirect
to the screen. Default: when the input filename is “input.dat”,
then the output filename defaults to “output.dat”. Otherwise, the
output filename defaults to the the input filename (subtracting
any ”.in” or ”.dat” suffix) plus ”.out”</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-p">
<span id="cmdoption-psi4--prefix"></span><code class="descname">-p</code><code class="descclassname"> <prefix></code><code class="descclassname">, </code><code class="descname">--prefix</code><code class="descclassname"> <prefix></code><a class="headerlink" href="#cmdoption-psi4-p" title="Permalink to this definition">¶</a></dt>
<dd><p>Prefix for psi files. Default: psi</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-s">
<span id="cmdoption-psi4--scratch"></span><code class="descname">-s</code><code class="descclassname"> <name></code><code class="descclassname">, </code><code class="descname">--scratch</code><code class="descclassname"> <name></code><a class="headerlink" href="#cmdoption-psi4-s" title="Permalink to this definition">¶</a></dt>
<dd><p>This overrides the value of <span class="target" id="index-9"></span><a class="reference internal" href="#envvar-PSI_SCRATCH"><code class="xref std std-envvar docutils literal"><span class="pre">PSI_SCRATCH</span></code></a> and provides
a path to the location of scratch files</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4--new-plugin">
<code class="descname">--new-plugin</code><code class="descclassname"> <name></code><a class="headerlink" href="#cmdoption-psi4--new-plugin" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a new directory <name> with files for writing a
new plugin. An additional argument specifies a template
to use, for example: <code class="docutils literal"><span class="pre">--new-plugin</span> <span class="pre">name</span> <span class="pre">+mointegrals</span></code>.
See Sec. <a class="reference internal" href="plugins.html#sec-plugins"><span>Plugins: Adding New Functionality to Psi4</span></a> for available templates.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-v">
<span id="cmdoption-psi4--verbose"></span><code class="descname">-v</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--verbose</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-v" title="Permalink to this definition">¶</a></dt>
<dd><p>Print a lot of information, including the Psithon translation of the input file</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-V">
<span id="cmdoption-psi4--version"></span><code class="descname">-V</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--version</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-V" title="Permalink to this definition">¶</a></dt>
<dd><p>Print version information.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-psi4-w">
<span id="cmdoption-psi4--wipe"></span><code class="descname">-w</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--wipe</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-psi4-w" title="Permalink to this definition">¶</a></dt>
<dd><p>Clean out scratch area.</p>
</dd></dl>
</div>
<div class="section" id="environment-variables">
<span id="sec-environmentvariables"></span><h2>Environment Variables<a class="headerlink" href="#environment-variables" title="Permalink to this headline">¶</a></h2>
<p>These environment variables will influence <span class="sc">Psi4</span>‘s behavior.</p>
<dl class="envvar">
<dt id="envvar-MKL_NUM_THREADS">
<code class="descname">MKL_NUM_THREADS</code><a class="headerlink" href="#envvar-MKL_NUM_THREADS" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of threads to use by operations with Intel threaded BLAS libraries.</p>
</dd></dl>
<dl class="envvar">
<dt id="envvar-OMP_NESTED">
<code class="descname">OMP_NESTED</code><a class="headerlink" href="#envvar-OMP_NESTED" title="Permalink to this definition">¶</a></dt>
<dd><p>Do access nested DGEMM in OpenMP sections in DFMP2 for multi-socket
platforms. This is very low-level access to OpenMP functions for
experienced programmers. Users should leave this variable unset or set
to <code class="docutils literal"><span class="pre">False</span></code>.</p>
</dd></dl>
<dl class="envvar">
<dt id="envvar-OMP_NUM_THREADS">
<code class="descname">OMP_NUM_THREADS</code><a class="headerlink" href="#envvar-OMP_NUM_THREADS" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of threads to use by modules with OpenMP threading.</p>
</dd></dl>
<dl class="envvar">
<dt id="envvar-PATH">
<code class="descname">PATH</code><a class="headerlink" href="#envvar-PATH" title="Permalink to this definition">¶</a></dt>
<dd><p>Path for interfaced executables.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Configuring <span class="sc">Psi4</span> through <span class="target" id="index-10"></span><a class="reference internal" href="#envvar-PSIPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PSIPATH</span></code></a> is preferred
to modifying this environment variable.</p>
</div>
<p>To run Kállay’s MRCC program
(see <a class="reference internal" href="mrcc.html#sec-mrcc"><span>MRCC</span></a>), the <code class="docutils literal"><span class="pre">dmrcc</span></code> executable must be in <span class="target" id="index-11"></span><a class="reference internal" href="#envvar-PATH"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a>.
Likewise to run Grimme’s dftd3 program (see <a class="reference internal" href="dftd3.html#sec-dftd3"><span>dftd3</span></a>), the
<code class="docutils literal"><span class="pre">dftd3</span></code> executable must be in <span class="target" id="index-12"></span><a class="reference internal" href="#envvar-PATH"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a>.</p>
</dd></dl>
<dl class="envvar">
<dt id="envvar-PSI_SCRATCH">
<code class="descname">PSI_SCRATCH</code><a class="headerlink" href="#envvar-PSI_SCRATCH" title="Permalink to this definition">¶</a></dt>
<dd><p>Directory where scratch files are written. Overrides settings in <code class="docutils literal"><span class="pre">~/.psi4rc</span></code>.</p>
</dd></dl>
<dl class="envvar">
<dt id="envvar-PSIPATH">
<code class="descname">PSIPATH</code><a class="headerlink" href="#envvar-PSIPATH" title="Permalink to this definition">¶</a></dt>
<dd><p>Path in which <span class="sc">Psi4</span> looks for user extensions to the built-in
libraries. Specifically, directories containing
<a class="reference internal" href="basissets.html#sec-basisuserdefined"><span>user basis sets</span></a>,
<a class="reference internal" href="libefp.html#sec-findingefpfragments"><span>EFP fragments</span></a>,
<a class="reference internal" href="quickadddatabase.html#sec-createdatabase"><span>databases</span></a>,
<a class="reference internal" href="plugins.html#sec-plugins"><span>plugins</span></a>, and
interfaced executables (
<code class="docutils literal"><span class="pre">dmrcc</span></code> for <a class="reference internal" href="mrcc.html#sec-mrcc"><span>MRCC</span></a> and
<code class="docutils literal"><span class="pre">dftd3</span></code> for <a class="reference internal" href="dftd3.html#sec-dftd3"><span>DFTD3</span></a>
) should be placed in this colon-separated list.</p>
<p><span class="sc">Psi4</span> is designed so that user extensions that are findable through
<span class="target" id="index-13"></span><a class="reference internal" href="#envvar-PSIPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PSIPATH</span></code></a> can be used in input files entirely like their
built-in counterparts, without additional tagging as non-standard.</p>
<p>The typical search path is first the built-in libraries, next each
<span class="target" id="index-14"></span><a class="reference internal" href="#envvar-PSIPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PSIPATH</span></code></a> directory in order, and finally the execution
directory (I won’t swear everything tacks on the execution directory).</p>
<p>Path in which the Python interpreter looks for modules to import. For
<span class="sc">Psi4</span>, these are generally plugins (see <a class="reference internal" href="plugins.html#sec-plugins"><span>Plugins: Adding New Functionality to Psi4</span></a>) or databases.</p>
<p>Modify <span class="target" id="index-15"></span><a class="reference internal" href="#envvar-PSIPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PSIPATH</span></code></a> though normal Linux shell commands before invoking <code class="docutils literal"><span class="pre">psi4</span></code></p>
<div class="highlight-python"><div class="highlight"><pre># csh, tcsh
>>> setenv PSIPATH /home/user/psiadditions:/home/user/gbs
# bash
>>> export PSIPATH=/home/user/psiadditions:/home/user/gbs
</pre></div>
</div>
</dd></dl>
<dl class="envvar">
<dt id="envvar-PYTHONPATH">
<code class="descname">PYTHONPATH</code><a class="headerlink" href="#envvar-PYTHONPATH" title="Permalink to this definition">¶</a></dt>
<dd><p>Path in which the Python interpreter looks for modules to import. For
<span class="sc">Psi4</span>, these are generally plugins (see <a class="reference internal" href="plugins.html#sec-plugins"><span>Plugins: Adding New Functionality to Psi4</span></a>) or databases.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Configuring <span class="sc">Psi4</span> through <span class="target" id="index-16"></span><a class="reference internal" href="#envvar-PSIPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PSIPATH</span></code></a> is preferred
to modifying this environment variable.</p>
</div>
<p>Modification of <span class="target" id="index-17"></span><a class="reference internal" href="#envvar-PYTHONPATH"><code class="xref std std-envvar docutils literal"><span class="pre">PYTHONPATH</span></code></a> can be done in three ways, equivalently.</p>
<ul>
<li><p class="first">Normal Linux shell commands. First line for C shell; second for bash.</p>
<div class="highlight-python"><div class="highlight"><pre>setenv PYTHONPATH /home/user/psiadditions:$PYTHONPATH
PYTHONPATH=/home/user/psiadditions:$PYTHONPATH; export PYTHONPATH
</pre></div>
</div>
</li>
<li><p class="first">Place the path in the <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> file so that it is available for
every <span class="sc">Psi4</span> instance.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">'/home/user/psiadditions'</span><span class="p">)</span>
</pre></div>
</div>
</li>
<li><p class="first">Place the path in the input file, either absolute or relative.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">'../../psiadditions'</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">'/home/user/psiadditions'</span><span class="p">)</span>
</pre></div>
</div>
</li>
</ul>
</dd></dl>
<dl class="envvar">
<dt id="envvar-PSIDATADIR">
<code class="descname">PSIDATADIR</code><a class="headerlink" href="#envvar-PSIDATADIR" title="Permalink to this definition">¶</a></dt>
<dd><p>Path in which the <span class="sc">Psi4</span> executable looks for its non-compiled
dependencies (<em>i.e.</em>, Python driver, basis sets, databases, <em>etc.</em>).
Not used when running from an installed (<code class="docutils literal"><span class="pre">make</span> <span class="pre">install</span></code>) executable,
so this variable is relevant primarily to developers running the
executable directly from the compilation directory. Value should be set
to directory containing driver, basis, <em>etc.</em> directories, generally
<code class="docutils literal"><span class="pre">psi4/lib</span></code>.</p>
</dd></dl>
<style type="text/css"><!--
.green {color: red;}
.sc {font-variant: small-caps;}
--></style></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="#">Installation and Runtime Configuration</a><ul>
<li><a class="reference internal" href="#obtaining-psifour">Obtaining <span class="sc">Psi4</span></a></li>
<li><a class="reference internal" href="#installing-from-binary">Installing from Binary</a></li>
<li><a class="reference internal" href="#compiling-and-installing-from-source">Compiling and Installing from Source</a></li>
<li><a class="reference internal" href="#scratch-files-and-the-psirc-file">Scratch Files and the <code class="docutils literal"><span class="pre">~/.psi4rc</span></code> File</a></li>
<li><a class="reference internal" href="#threading">Threading</a></li>
<li><a class="reference internal" href="#command-line-options">Command Line Options</a></li>
<li><a class="reference internal" href="#environment-variables">Environment Variables</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="cfour_table_grad.html"
title="previous chapter"><no title></a></p>
<h4>Next topic</h4>
<p class="topless"><a href="conda.html"
title="next chapter">Binary Distribution</a></p>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/external.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
<p class="searchtip" style="font-size: 90%">
Enter search terms or a module, class or function name.
</p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="relbar-bottom">
<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="contents.html" title="Table Of Contents"
>toc</a> </li>
<li class="right" >
<a href="conda.html" title="Binary Distribution"
>next</a> </li>
<li class="right" >
<a href="cfour_table_grad.html" title="<no title>"
>previous</a> </li>
<li><a href="index.html">Psi4 []</a> » </li>
</ul>
</div>
</div>
<div class="footer" role="contentinfo">
© Copyright 2015, The Psi4 Project.
Last updated on Tuesday, 12 January 2016 03:10PM.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.3.
</div>
<!-- cloud_sptheme 1.3 -->
</body>
</html>
|