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<div class="section" id="molecule-and-geometry-specification">
<span id="sec-moleculespecification"></span><span id="index-0"></span><h1>Molecule and Geometry Specification<a class="headerlink" href="#molecule-and-geometry-specification" title="Permalink to this headline">¶</a></h1>
<div class="section" id="coordinates">
<h2>Coordinates<a class="headerlink" href="#coordinates" title="Permalink to this headline">¶</a></h2>
<p><span class="sc">Psi4</span> has a very flexible input parser that allows the user to provide
geometries as Cartesian coordinates, Z-matrix variables, or a combination of
both. The use of fixed values and variables are supported for both. For
example, the geometry for H<sub>2</sub> can be specified a number of ways, using the
<code class="samp docutils literal"><span class="pre">molecule</span> <em><span class="pre">optional_molecule_name</span></em> <span class="pre">{...}</span></code> block.</p>
<div class="highlight-python"><div class="highlight"><pre>molecule {
H
H 1 0.9
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule {
H
H 1 r
r = 0.9
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule {
H1
H2 H1 0.9
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule {
H 0.0 0.0 0.0
H 0.0 0.0 0.9
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule {
H 0.0 0.0 0.0
H 0.0 0.0 r
r = 0.9
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule {
H 0.0 0.0 -r
H 0.0 0.0 r
r = 0.45
}
</pre></div>
</div>
<p>Blank lines are ignored and, unlike regular Python syntax, indentation within
the molecule block does not matter, although the <code class="docutils literal"><span class="pre">molecule</span></code> keyword itself must
be aligned within the input according to standard Python syntax. For more
examples of geometry specification, see the <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/mints1/input.dat">mints1</a> input file in the samples
folder. It is also possible to mix Cartesian and Z-matrix geometry
specifications, as demonstrated in the <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/mints4/input.dat">mints4</a> and
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/mints6/input.dat">mints6</a> sample input files. For example, consider the following
geometry specification, taken from the <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/mints6/input.dat">mints6</a> input:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule alanine {
N -1.527107413251 0.745960643462 0.766603000356
C -0.075844098953 0.811790225041 0.711418672248
C 0.503195220163 -0.247849447550 -0.215671574613
O -0.351261319421 -0.748978309671 -1.089590304723
O 1.639498336738 -0.571249748886 -0.174705953194
H -1.207655674855 -0.365913941094 -0.918035522052
# First, remove the H from the alpha carbon. This line could be deleted
# and is only included for completeness
#H 0.429560656538 0.717651915252 1.673774709694
# Now patch it, using a Z Matrix specification. This patch can be applied
# anywhere in the coord specification, as long as it appears lower than
# the atoms referenced, as is usual for Z-Matrices
C 2 rCC 3 aCCC 1 dCCCN
H 7 rCH1 2 aHCC1 3 dHCCC1
H 7 rCH2 2 aHCC2 3 dHCCC2
H 7 rCH3 2 aHCC3 3 dHCCC3
H 0.221781602033 1.772570540211 0.286988509018
H -1.833601608592 0.108401996052 1.481873213172
H -1.925572581453 1.640882152784 0.986471814808
aCCC = 108.0
rCC = 1.4
dCCCN = 120
rCH1 = 1.08
rCH2 = 1.08
rCH3 = 1.08
aHCC1 = 109.0
aHCC2 = 109.0
aHCC3 = 109.0
dHCCC1 = 0.0
dHCCC2 = 120.0
dHCCC3 = 240.0
}
</pre></div>
</div>
<p>Here, we remove the hydrogen from the alpha carbon of glycine and replace it
with a methyl group. Applying this patch using Cartesian coordinates is
difficult, because it depends on the orientation of the existing glycine unit.
In this example, we use Z-Matrix coordinates to define the methyl group, and
define the orientation in terms of the existing glycine Cartesian coordinates
which is much easier to visualize than the corresponding Cartesian-only
approach.</p>
<span class="target" id="sec-multiplemolecules"><span id="index-1"></span></span></div>
<div class="section" id="molecule-keywords">
<span id="sec-moleculekeywords"></span><span id="index-2"></span><h2>Molecule Keywords<a class="headerlink" href="#molecule-keywords" title="Permalink to this headline">¶</a></h2>
<p>In addition to specifying the geometry, additional information can be
provided in the molecule block <code class="samp docutils literal"><span class="pre">molecule</span> <em><span class="pre">optional_molecule_name</span></em> <span class="pre">{...}</span></code>.</p>
<dl class="docutils">
<dt><strong>Charge & Multiplicity</strong></dt>
<dd>If two integers <code class="samp docutils literal"><em><span class="pre">charge</span></em> <em><span class="pre">multiplicity</span></em></code> are encountered on any
line of the molecule block, they are interpreted as the molecular charge
and multiplicity (<img class="math" src="_images/math/621d701fcdd14a2b0c44c276ca3f09f8b34a0101.png" alt="2 M_s + 1" style="vertical-align: -3px"/>), respectively. For multi-fragment
complexes, each fragment can have a <code class="samp docutils literal"><em><span class="pre">charge</span></em> <em><span class="pre">multiplicity</span></em></code> line.</dd>
<dt><strong>Units</strong></dt>
<dd>By default, Ångström units are used; this is changed by adding
a line that reads <code class="samp docutils literal"><span class="pre">units</span> <em><span class="pre">spec</span></em></code>, where <code class="samp docutils literal"><em><span class="pre">spec</span></em></code> is one
of <code class="docutils literal"><span class="pre">ang</span></code>, <code class="docutils literal"><span class="pre">angstrom</span></code>, <code class="docutils literal"><span class="pre">a.u.</span></code>, <code class="docutils literal"><span class="pre">au</span></code>, or <code class="docutils literal"><span class="pre">bohr</span></code>.</dd>
<dt><strong>Orientation</strong></dt>
<dd>Certain computations require that the molecule is not reoriented. This
can be achieved by adding either <code class="docutils literal"><span class="pre">no_reorient</span></code> or <code class="docutils literal"><span class="pre">noreorient</span></code>.
To prevent even recentering of the molecule, add <code class="docutils literal"><span class="pre">no_com</span></code> or <code class="docutils literal"><span class="pre">nocom</span></code>.</dd>
<dt><strong>PubChem</strong></dt>
<dd>A line reading <code class="samp docutils literal"><span class="pre">pubchem:</span><em><span class="pre">mol</span></em></code> fetches the geometry for molecule
<code class="samp docutils literal"><em><span class="pre">mol</span></em></code> from the PubChem database, where <code class="samp docutils literal"><em><span class="pre">mol</span></em></code> is either
the IUPAC molecule name or the CID number. See <a class="reference internal" href="#sec-pubchem"><span>PubChem Database</span></a> for
details.</dd>
<dt><strong>Symmetry</strong></dt>
<dd>The symmetry can be specified by a line reading <code class="samp docutils literal"><span class="pre">symmetry</span>
<em><span class="pre">symbol</span></em></code>, where <code class="samp docutils literal"><em><span class="pre">symbol</span></em></code> is the Schönflies symbol
of the (Abelian) point group to use for the computation, one of one of
<code class="docutils literal"><span class="pre">c1</span></code>, <code class="docutils literal"><span class="pre">c2</span></code>, <code class="docutils literal"><span class="pre">ci</span></code>, <code class="docutils literal"><span class="pre">cs</span></code>, <code class="docutils literal"><span class="pre">d2</span></code>, <code class="docutils literal"><span class="pre">c2h</span></code>, <code class="docutils literal"><span class="pre">c2v</span></code>, or <code class="docutils literal"><span class="pre">d2h</span></code>.
This need not be specified, as the molecular symmetry is automatically
detected by <span class="sc">Psi4</span>. See <a class="reference internal" href="#sec-symmetry"><span>Symmetry</span></a> for details.</dd>
<dt><strong>Fragments</strong></dt>
<dd>A line reading <code class="docutils literal"><span class="pre">--</span></code> is interpreted as the separator between two non-covalently
bound molecular fragments. See <a class="reference internal" href="#sec-fragments"><span>Non-Covalently Bonded Molecule Fragments</span></a> for details.</dd>
</dl>
</div>
<div class="section" id="multiple-molecules">
<h2>Multiple Molecules<a class="headerlink" href="#multiple-molecules" title="Permalink to this headline">¶</a></h2>
<p>To facilitate more elaborate computations, it is possible to provide a name for
each molecule and tell <span class="sc">Psi4</span> which one should be used in a given
calculation. For example, consider the following input file:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule h2 {
H
H 1 0.9
}
set basis cc-pvdz
set reference rhf
energy('scf')
clean()
molecule h {
H
}
set basis cc-pvdz
set reference uhf
energy('scf')
</pre></div>
</div>
<p>Here, two separate jobs are performed on two different molecules; the first is
performed on H<sub>2</sub>, while the second is for H atom. The last molecule to be
specified is the “active” molecule by default. To explicitly activate a named
molecule, the activate command is provided. With it, the above input
file can be equivalently written as follows:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule h2 {
H
H 1 0.9
}
molecule h {
H
}
activate(h2)
set basis cc-pvdz
set reference rhf
energy('scf')
clean()
activate(h)
set basis cc-pvdz
set reference uhf
energy('scf')
</pre></div>
</div>
<p>Note that whenever the molecule is changed, the basis set must be specified
again. <a class="reference internal" href="psithoninput.html#sec-jobcontrol"><span>Job Control Keywords</span></a> provides more details about the job control
and calculation keywords used in the above examples.</p>
</div>
<div class="section" id="ghost-atoms">
<span id="sec-ghosts"></span><span id="index-3"></span><h2>Ghost Atoms<a class="headerlink" href="#ghost-atoms" title="Permalink to this headline">¶</a></h2>
<p>While many common computations, particularly SAPT and counterpoise corrections, can
be greatly simplified using the notation described in <a class="reference internal" href="#sec-fragments"><span>Non-Covalently Bonded Molecule Fragments</span></a>,
manual specification of ghost atoms is sometimes required. Either</p>
<div class="highlight-python"><div class="highlight"><pre>molecule he2 {
He
Gh(He) 1 2.0
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule he2 {
He
@He 1 2.0
}
</pre></div>
</div>
<p>will generate a helium dimer with the second atom ghosted, <em>i.e.</em>, possessing
basis functions but no electrons or nuclear charge. See <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/dfmp2_1/input.dat">dfmp2_1</a>
and <a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/ghosts/input.dat">ghosts</a> for a demonstration of both mechanisms for specifying
ghost atoms.</p>
</div>
<div class="section" id="pubchem-database">
<span id="sec-pubchem"></span><span id="index-4"></span><h2><a class="reference external" href="http://pubchem.ncbi.nlm.nih.gov/">PubChem</a> Database<a class="headerlink" href="#pubchem-database" title="Permalink to this headline">¶</a></h2>
<p>Obtaining rough starting guess geometries can be burdensome. The Z-matrix
coordinate system was designed to provide chemists with an intuitive method for
guessing structures in terms of bond lengths and angles. While Z-matrix input is
intuitive for small molecules with few degrees of freedom, it quickly becomes
laborious as the system size grows. To obtain a reasonable starting guess
geometry, <span class="sc">Psi4</span> can take a chemical name as input; this is then used
to attempt to retrieve Cartesian coordinates from the <a class="reference internal" href="bibliography.html#pubchem" id="id1">[PubChem]</a> database.</p>
<p>For example, to run a computation on benzene, we can use the following molecule specification:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule benzene {
pubchem:benzene
}
</pre></div>
</div>
<p>If the computer is connected to the internet, the above code will instruct
<span class="sc">Psi4</span> to search PubChem for a starting structure. The search is actually
performed for compounds whose name <em>contains</em> “benzene”, so multiple
entries will be returned. If the name provided (“benzene” in the above
example) exactly matches one of the results, that entry will be used. If no
exact match is found the results, along with a unique chemical identifier
(CID), are printed to the output file, prompting the user to provide a more
specific name. For example, if we know that we want to run a computation on a
compound whose name(s) contain “benzene”, but we’re not sure of the exact IUPAC
name, the following input can be used:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule benzene {
pubchem:benzene*
}
</pre></div>
</div>
<p>Appending the “*” prevents an exact match from being found and, at the time
of writing, the following results are displayed in the output file:</p>
<div class="highlight-python"><div class="highlight"><pre>Chemical ID IUPAC Name
241 benzene
7371 benzenesulfonic acid
91526 benzenesulfonate
244 phenylmethanol
727 1,2,3,4,5,6-hexachlorocyclohexane
240 benzaldehyde
65723 benzenesulfonohydrazide
74296 N-phenylbenzenesulfonamide
289 benzene-1,2-diol
243 benzoic acid
7370 benzenesulfonamide
636822 1,2,4-trimethoxy-5-[(E)-prop-1-enyl]benzene
7369 benzenesulfonyl chloride
12932 N-[2-di(propan-2-yloxy)phosphinothioylsulfanylethyl]benzenesulfonamide
7505 benzonitrile
78438 N-[anilino(phenyl)phosphoryl]aniline
12581 3-phenylpropanenitrile
517327 sodium benzenesulfonate
637563 1-methoxy-4-[(E)-prop-1-enyl]benzene
252325 [(E)-prop-1-enyl]benzene
</pre></div>
</div>
<p>Note that some of these results do not contain the string “benzene”; these
compounds have synonyms containing that text. We can now replace the
“benzene*” in the input file with one of the above compounds using either the
IUPAC name or the CID provided in the list, <em>viz</em>:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule benzene {
pubchem:637563
}
</pre></div>
</div>
<p>or</p>
<div class="highlight-python"><div class="highlight"><pre>molecule benzene {
pubchem:1-methoxy-4-[(E)-prop-1-enyl]benzene
}
</pre></div>
</div>
<p>Some of the structures in the database are quite loosely optimized and do not
have the correct symmetry. Before starting the computation, <span class="sc">Psi4</span> will
check to see if the molecule is close to having each of the possible
symmetries, and will adjust the structure accordingly so that the maximum
symmetry is utilized.</p>
<p>The standard keywords, described in <a class="reference internal" href="#sec-moleculekeywords"><span>Molecule Keywords</span></a>, can be
used in conjuction to specify charge, multiplicity, symmetry to use, <em>etc.</em> .</p>
</div>
<div class="section" id="symmetry">
<span id="sec-symmetry"></span><span id="index-5"></span><h2>Symmetry<a class="headerlink" href="#symmetry" title="Permalink to this headline">¶</a></h2>
<p>For efficiency, <span class="sc">Psi4</span> can utilize the largest Abelian subgroup of the full
point group of the molecule. Concomitantly, a number of quantities, such as
<a class="reference internal" href="autodoc_glossary_options_c.html#term-socc-globals"><span class="xref std std-term">SOCC</span></a> and <a class="reference internal" href="autodoc_glossary_options_c.html#term-docc-globals"><span class="xref std std-term">DOCC</span></a>, are arrays whose entries pertain to irreducible
representations (irreps) of the molecular point group. Ordering of irreps
follows the convention used in Cotton’s <cite>Chemical Applications of Group
Theory</cite>, as detailed in Table <a class="reference internal" href="#table-irrepordering"><span>Irreps</span></a>. We refer to this
convention as “Cotton Ordering” hereafter.</p>
<table border="1" class="docutils" id="id2">
<span id="table-irrepordering"></span><caption><span class="caption-text">Ordering of irreducible representations (irreps) used in <span class="sc">Psi4</span></span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
<colgroup>
<col width="12%" />
<col width="9%" />
<col width="12%" />
<col width="12%" />
<col width="12%" />
<col width="9%" />
<col width="12%" />
<col width="12%" />
<col width="12%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Point Group</th>
<th class="head">1</th>
<th class="head">2</th>
<th class="head">3</th>
<th class="head">4</th>
<th class="head">5</th>
<th class="head">6</th>
<th class="head">7</th>
<th class="head">8</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td><img class="math" src="_images/math/a7223a037dfd9076deee6e5754c08434bebef462.png" alt="C_1" style="vertical-align: -4px"/></td>
<td><img class="math" src="_images/math/565d5265a5771ce110bca359c85a858ec1d8e7e2.png" alt="A" style="vertical-align: 0px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-odd"><td><img class="math" src="_images/math/9454726fb4304aba31c8af0f71903451758cab8d.png" alt="C_i" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/f4a6d6db1509304e0367cffd1ad3942a61a14579.png" alt="A_g" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/52085ea8ac3d6d40d4a0447ccc8d12ff887373a2.png" alt="A_u" style="vertical-align: -3px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-even"><td><img class="math" src="_images/math/5397631d0b2847b2a135d492176b9e0d5ef61ab2.png" alt="C_2" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/565d5265a5771ce110bca359c85a858ec1d8e7e2.png" alt="A" style="vertical-align: 0px"/></td>
<td><img class="math" src="_images/math/fd8a1eb9153f0dc573e5ebe023a59474dadd17ef.png" alt="B" style="vertical-align: 0px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-odd"><td><img class="math" src="_images/math/2c450bda9bb1b22b4fa818fdc3269030fe3d6296.png" alt="C_s" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/54a22b2b19871920b9012e66f9f5034a8ee88579.png" alt="A'" style="vertical-align: 0px"/></td>
<td><img class="math" src="_images/math/b51ab8e1c35fd093ac5123c62f52846eadce707e.png" alt="A''" style="vertical-align: 0px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-even"><td><img class="math" src="_images/math/a9dc0a375d48d53b36991cb6ee3f3f5b77d3216b.png" alt="D_2" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/565d5265a5771ce110bca359c85a858ec1d8e7e2.png" alt="A" style="vertical-align: 0px"/></td>
<td><img class="math" src="_images/math/fd0669720606eebd9d117082f589c6e9807af337.png" alt="B_1" style="vertical-align: -4px"/></td>
<td><img class="math" src="_images/math/7dcb548591442130bc2b7fe439b00cda59130bd1.png" alt="B_2" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/ae7d48bcfd1c89800c04057077faeda3725ca7a7.png" alt="B_3" style="vertical-align: -3px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-odd"><td><img class="math" src="_images/math/ab44cf29f6b7cf2559186d6ec00af45f66958751.png" alt="C_{2v}" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/9553af89635e87864e5ed39e397c77d5dbb2515e.png" alt="A_1" style="vertical-align: -4px"/></td>
<td><img class="math" src="_images/math/7354b4768908022e9709a2d4cb5cb8c3284652b7.png" alt="A_2" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/fd0669720606eebd9d117082f589c6e9807af337.png" alt="B_1" style="vertical-align: -4px"/></td>
<td><img class="math" src="_images/math/7dcb548591442130bc2b7fe439b00cda59130bd1.png" alt="B_2" style="vertical-align: -3px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-even"><td><img class="math" src="_images/math/dc186a22a21ff3eb15c312a82a0fc5ee7b5fa531.png" alt="C_{2h}" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/f4a6d6db1509304e0367cffd1ad3942a61a14579.png" alt="A_g" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/44b4617ca0c2015b9f7183bac061074321bacc59.png" alt="B_g" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/52085ea8ac3d6d40d4a0447ccc8d12ff887373a2.png" alt="A_u" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/865b4acf73ac24b56a7cd3a786e5147c39c75d2b.png" alt="B_u" style="vertical-align: -3px"/></td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr class="row-odd"><td><img class="math" src="_images/math/db75df3e2b5a073f500992eae10086986cebf33f.png" alt="D_{2h}" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/f4a6d6db1509304e0367cffd1ad3942a61a14579.png" alt="A_g" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/5de7e078e4b135fcab413a3bb4046ff175f73cb8.png" alt="B_{1g}" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/4ad37e66de065e5d1ace9d8ae6ecaf09d840d6d7.png" alt="B_{2g}" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/16a1e9d0f23b7aba149d97f6bbae37bad3dbaa18.png" alt="B_{3g}" style="vertical-align: -6px"/></td>
<td><img class="math" src="_images/math/52085ea8ac3d6d40d4a0447ccc8d12ff887373a2.png" alt="A_u" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/386a5958a2f5128f9753c1ff2842f156582171fa.png" alt="B_{1u}" style="vertical-align: -4px"/></td>
<td><img class="math" src="_images/math/43fc576c686d2325ef1861626de149aa5d638f88.png" alt="B_{2u}" style="vertical-align: -3px"/></td>
<td><img class="math" src="_images/math/387f8bd7544e07b1e920eb832333b1e2cbab1915.png" alt="B_{3u}" style="vertical-align: -3px"/></td>
</tr>
</tbody>
</table>
<p>For example, water (<img class="math" src="_images/math/ab44cf29f6b7cf2559186d6ec00af45f66958751.png" alt="C_{2v}" style="vertical-align: -3px"/> symmetry) has three doubly occupied <img class="math" src="_images/math/9553af89635e87864e5ed39e397c77d5dbb2515e.png" alt="A_1" style="vertical-align: -4px"/>
orbitals, as well as one each of <img class="math" src="_images/math/fd0669720606eebd9d117082f589c6e9807af337.png" alt="B_1" style="vertical-align: -4px"/> and <img class="math" src="_images/math/7dcb548591442130bc2b7fe439b00cda59130bd1.png" alt="B_2" style="vertical-align: -3px"/> symmetry; the
corresponding <a class="reference internal" href="autodoc_glossary_options_c.html#term-docc-globals"><span class="xref std std-term">DOCC</span></a> array is therefore:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">DOCC</span> <span class="o">=</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span>
</pre></div>
</div>
<p>Although <span class="sc">Psi4</span> will detect the symmetry automatically, and use the largest
possible Abelian subgroup, the user might want to run in a lower point group.
To do this the molecule keyword <code class="samp docutils literal"><span class="pre">symmetry</span> <em><span class="pre">symbol</span></em></code> can be used
(see <a class="reference internal" href="#sec-moleculekeywords"><span>Molecule Keywords</span></a>). In most cases the standard
Schönflies symbol (one of <code class="docutils literal"><span class="pre">c1</span></code>, <code class="docutils literal"><span class="pre">c2</span></code>, <code class="docutils literal"><span class="pre">ci</span></code>, <code class="docutils literal"><span class="pre">cs</span></code>, <code class="docutils literal"><span class="pre">d2</span></code>,
<code class="docutils literal"><span class="pre">c2h</span></code>, <code class="docutils literal"><span class="pre">c2v</span></code>, <code class="docutils literal"><span class="pre">d2h</span></code> will suffice for <code class="samp docutils literal"><em><span class="pre">symbol</span></em></code>.
For certain computations, the user might want to specify which particular
subgroup is to be used by appending a unique axis specifier. For example when
running a computation on a molecule with <img class="math" src="_images/math/db75df3e2b5a073f500992eae10086986cebf33f.png" alt="D_{2h}" style="vertical-align: -3px"/> symmetry in <img class="math" src="_images/math/ab44cf29f6b7cf2559186d6ec00af45f66958751.png" alt="C_{2v}" style="vertical-align: -3px"/>, the
<img class="math" src="_images/math/5397631d0b2847b2a135d492176b9e0d5ef61ab2.png" alt="C_2" style="vertical-align: -3px"/> axis can be chosen as either the <img class="math" src="_images/math/86e784d473f5fc5713b6ad4bea7af624b76966c2.png" alt="x" style="vertical-align: 0px"/>, the <img class="math" src="_images/math/95ca3c6a1fbeaaafe5800c3269c4c9c2cf2e5406.png" alt="y" style="vertical-align: -4px"/>, or the <img class="math" src="_images/math/4764300df3b118f2c580952e9fb04e7cd7943ba5.png" alt="z" style="vertical-align: 0px"/>; these can
be specified by requesing the symmetry as <code class="docutils literal"><span class="pre">c2vx</span></code>, <code class="docutils literal"><span class="pre">c2vy</span></code>, or <code class="docutils literal"><span class="pre">c2vz</span></code>, respectively.
Likewise the <code class="docutils literal"><span class="pre">c2x</span></code>, <code class="docutils literal"><span class="pre">c2y</span></code>, <code class="docutils literal"><span class="pre">c2z</span></code>, <code class="docutils literal"><span class="pre">c2hx</span></code>, <code class="docutils literal"><span class="pre">c2hy</span></code>, and <code class="docutils literal"><span class="pre">c2hz</span></code>
labels are valid. For <img class="math" src="_images/math/2c450bda9bb1b22b4fa818fdc3269030fe3d6296.png" alt="C_s" style="vertical-align: -3px"/> symmetry the labels <code class="docutils literal"><span class="pre">csx</span></code>, <code class="docutils literal"><span class="pre">csy</span></code>, and
<code class="docutils literal"><span class="pre">csz</span></code> request the <img class="math" src="_images/math/4674377e6a0143771ca8b8e0d78ec4fd4b14779c.png" alt="yz" style="vertical-align: -4px"/>, <img class="math" src="_images/math/cd12011742e99d945f955c9dc4925a7134fd6eb1.png" alt="xz" style="vertical-align: 0px"/>, and <img class="math" src="_images/math/8d614ac07c67f7071f6943e0c55a674e0aacc62a.png" alt="xy" style="vertical-align: -4px"/> planes be used as the mirror plane,
respectively. If no unique axis is specified, <span class="sc">Psi4</span> will choose an appropriate
subgroup.</p>
<p>Certain types of finite difference computations, such as numerical vibrational
frequencies, might lower the symmetry of the molecule. When this happens
symmetry-dependent arrays, such as <a class="reference internal" href="autodoc_glossary_options_c.html#term-socc-globals"><span class="xref std std-term">SOCC</span></a>, are automatically remapped
to the lower symmetry. For example, if we were to investigate the <img class="math" src="_images/math/6aa4d84e04ed966cdf22f2b78a0dfe5afeb5e83f.png" alt="^2B_1" style="vertical-align: -4px"/>
state of water cation, we can specify</p>
<blockquote>
<div>SOCC = [0, 0, 1, 0]</div></blockquote>
<p>in the input file. If any ensuing computations lower the symmetry, the above
array will be appropriately remapped. For example, reducing the symmetry to
<img class="math" src="_images/math/2c450bda9bb1b22b4fa818fdc3269030fe3d6296.png" alt="C_s" style="vertical-align: -3px"/> (with the molecular plane defining the mirror plane), the above
array will be automatically interpreted as:</p>
<blockquote>
<div>SOCC = [0, 1]</div></blockquote>
<p>Some caution is required, however. The <img class="math" src="_images/math/82ce48270cf3019ea249ecfcac4bc041209249c3.png" alt="^2A_1" style="vertical-align: -4px"/> state can be obtained with
the</p>
<blockquote>
<div>SOCC = [1, 0, 0, 0]</div></blockquote>
<p>specification, which would become</p>
<blockquote>
<div>SOCC = [1, 0]</div></blockquote>
<p>under the above-mentioned reduction in symmetry. The <img class="math" src="_images/math/5d16d7da0ae049589fcef59cc5e7be1ccaf76063.png" alt="^2B_2" style="vertical-align: -3px"/> state,
whose singly-occupied orbitals are</p>
<blockquote>
<div>SOCC = [0, 0, 0, 1]</div></blockquote>
<p>would be mapped to</p>
<blockquote>
<div>SOCC = [1, 0]</div></blockquote>
<p>which is the same occupation as the <img class="math" src="_images/math/82ce48270cf3019ea249ecfcac4bc041209249c3.png" alt="^2A_1" style="vertical-align: -4px"/> state. In this case, the
<img class="math" src="_images/math/82ce48270cf3019ea249ecfcac4bc041209249c3.png" alt="^2A_1" style="vertical-align: -4px"/> state is lower in energy, and is not problematic. The distorted
geometries for the <img class="math" src="_images/math/5d16d7da0ae049589fcef59cc5e7be1ccaf76063.png" alt="^2B_2" style="vertical-align: -3px"/> state are excited states that are subject to
variational collapse. One way to obtain reliable energies for these states is
to use a multi-state method; in this case it’s easier to run the entire
computation in the lowest symmetry needed during the finite difference
procedure.</p>
</div>
<div class="section" id="non-covalently-bonded-molecule-fragments">
<span id="sec-fragments"></span><span id="index-6"></span><h2>Non-Covalently Bonded Molecule Fragments<a class="headerlink" href="#non-covalently-bonded-molecule-fragments" title="Permalink to this headline">¶</a></h2>
<p><span class="sc">Psi4</span> has an extensive range of tools for treating non-covalent
intermolecular forces, including counterpoise corrections and symmetry adapted
perturbation theory methods. These require the definition of which fragments
are interacting within the complex. <span class="sc">Psi4</span> provides a very simple mechanism
for doing so: simply define the complex’s geometry using the standard
Cartesian, Z-matrix, or mixture thereof, specifications and then place two
dashes between nonbonded fragements. For example, to study the interaction
energy of ethane and ethyne molecules, we can use the following molecule
block:</p>
<div class="highlight-python"><div class="highlight"><pre>molecule eneyne {
0 1
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
0 1
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
}
</pre></div>
</div>
<p>In this case, the charge and multiplicity of each interacting fragment is
explicitly specified. If the charge and multiplicity are specified for the
first fragment, it is assumed to be the same for all fragments. When
considering interacting fragments, the overall charge is simply the sum of all
fragment charges, and any unpaired electrons are assumed to be coupled to
yield the highest possible <img class="math" src="_images/math/19bd28226d5c470d30f7497311211ab6221ac711.png" alt="M_s" style="vertical-align: -3px"/> value.</p>
<p>Having defined a molecule containing fragments like <code class="docutils literal"><span class="pre">eneyne</span></code> above, it
is a simple matter to perform calculations on only a subset of the
fragments. For instance, the commands below run a scf first on the ethene
fragment alone (<code class="docutils literal"><span class="pre">extract_subsets(1)</span></code> pulls out fragment 1 as Real atoms
and discards remaining fragments) and next on the ethene fragment with the
ethyne fragment ghosted (<code class="docutils literal"><span class="pre">extract_subsets(1,2)</span></code> pulls out fragment 1 as
Real atoms and sets fragment 2 as Ghost atoms). For beyond bimolecular
complexes, arrays can be used, e.g. <code class="docutils literal"><span class="pre">extract_subsets(2,[1,3])</span></code>:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">mA</span> <span class="o">=</span> <span class="n">eneyne</span><span class="o">.</span><span class="n">extract_subsets</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">energy</span><span class="p">(</span><span class="s">'scf'</span><span class="p">)</span>
<span class="n">clean</span><span class="p">()</span>
<span class="n">mAcp</span> <span class="o">=</span> <span class="n">eneyne</span><span class="o">.</span><span class="n">extract_subsets</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">)</span>
<span class="n">energy</span><span class="p">(</span><span class="s">'scf'</span><span class="p">)</span>
</pre></div>
</div>
<p>If the molecule contains fragments but is not conveniently ordered for the
<code class="docutils literal"><span class="pre">--</span></code> marker, the auto_fragment function can be applied, as shoown in
<a class="reference external" href="https://github.com/psi4/psi4public/blob/master/samples/pywrap-basis/input.dat">pywrap-basis</a>, to return as active molecule the previous
active molecule, only fragmented.</p>
</div>
<div class="section" id="advanced-python">
<h2>Advanced Python<a class="headerlink" href="#advanced-python" title="Permalink to this headline">¶</a></h2>
<p>A named molecule in an input file is a full-fledged instance of the
powerful <a class="reference internal" href="autodoc_psimod.html#sec-psimod-molecule"><span>C++ Molecule class</span></a>. Thus, all member
functions (that have been exported via Boost Python) documented thereat
are accessible through the handle <code class="samp docutils literal"><em><span class="pre">option_molecule_name</span></em></code> in
<code class="samp docutils literal"><span class="pre">molecule</span> <em><span class="pre">optional_molecule_name</span></em> <span class="pre">{...}</span></code>.</p>
<style type="text/css"><!--
.green {color: red;}
.sc {font-variant: small-caps;}
--></style></div>
</div>
</div>
</div>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Molecule and Geometry Specification</a><ul>
<li><a class="reference internal" href="#coordinates">Coordinates</a></li>
<li><a class="reference internal" href="#molecule-keywords">Molecule Keywords</a></li>
<li><a class="reference internal" href="#multiple-molecules">Multiple Molecules</a></li>
<li><a class="reference internal" href="#ghost-atoms">Ghost Atoms</a></li>
<li><a class="reference internal" href="#pubchem-database">PubChem Database</a></li>
<li><a class="reference internal" href="#symmetry">Symmetry</a></li>
<li><a class="reference internal" href="#non-covalently-bonded-molecule-fragments">Non-Covalently Bonded Molecule Fragments</a></li>
<li><a class="reference internal" href="#advanced-python">Advanced Python</a></li>
</ul>
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