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<div class="navpath"><b>sc</b>::<a class="el" href="classsc_1_1SimpleCo.html">SimpleCo</a>
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<h1>sc::SimpleCo Class Reference</h1><!-- doxytag: class="sc::SimpleCo" --><!-- doxytag: inherits="sc::IntCoor" -->The <a class="el" href="classsc_1_1SimpleCo.html" title="The SimpleCo abstract class describes a simple internal coordinate of a molecule...">SimpleCo</a> abstract class describes a simple internal coordinate of a molecule.
<a href="#_details">More...</a>
<p>
<code>#include <<a class="el" href="simple_8h_source.html">simple.h</a>></code>
<p>
<div class="dynheader">
Inheritance diagram for sc::SimpleCo:</div>
<div class="dynsection">
<p><center><img src="classsc_1_1SimpleCo.png" usemap="#sc::SimpleCo_map" border="0" alt=""></center>
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<p>
<a href="classsc_1_1SimpleCo-members.html">List of all members.</a><table border="0" cellpadding="0" cellspacing="0">
<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#586dd9e1bb276feb0b7d5d1535163156">SimpleCo</a> (int, const char *=0)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">This constructor takes an integer argument which is the number of atoms needed to describe the coordinate. <a href="#586dd9e1bb276feb0b7d5d1535163156"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="7d37707cc40982bd3618279c9c4c60d5"></a><!-- doxytag: member="sc::SimpleCo::SimpleCo" ref="7d37707cc40982bd3618279c9c4c60d5" args="(const Ref< KeyVal > &, int natom)" -->
</td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#7d37707cc40982bd3618279c9c4c60d5">SimpleCo</a> (const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1KeyVal.html">KeyVal</a> > &, int natom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">The <a class="el" href="classsc_1_1KeyVal.html" title="The KeyVal class is designed to simplify the process of allowing a user to specify...">KeyVal</a> constructor requires the number of atoms. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="6dbd635a6425345a2aab5a1d704eeba8"></a><!-- doxytag: member="sc::SimpleCo::natoms" ref="6dbd635a6425345a2aab5a1d704eeba8" args="() const " -->
int </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#6dbd635a6425345a2aab5a1d704eeba8">natoms</a> () const </td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Returns the number of atoms in the coordinate. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="af5648dcccfd8d318da90c4b003245c4"></a><!-- doxytag: member="sc::SimpleCo::operator[]" ref="af5648dcccfd8d318da90c4b003245c4" args="(int i) const " -->
int </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#af5648dcccfd8d318da90c4b003245c4">operator[]</a> (int i) const </td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Returns the index of the i'th atom in the coordinate. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#e5d77a1e7645a1ed3e8e6f7141f3408c">save_data_state</a> (<a class="el" href="classsc_1_1StateOut.html">StateOut</a> &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Save the base classes (with save_data_state) and the members in the same order that the <a class="el" href="classsc_1_1StateIn.html" title="Restores objects that derive from SavableState.">StateIn</a> CTOR initializes them. <a href="#e5d77a1e7645a1ed3e8e6f7141f3408c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="f961701f2e92400400ce6e50528367e1"></a><!-- doxytag: member="sc::SimpleCo::SimpleCo" ref="f961701f2e92400400ce6e50528367e1" args="(StateIn &)" -->
</td><td class="memItemRight" valign="bottom"><b>SimpleCo</b> (<a class="el" href="classsc_1_1StateIn.html">StateIn</a> &)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="b10f7f7009cfa5591a5f6e6a645c8359"></a><!-- doxytag: member="sc::SimpleCo::operator==" ref="b10f7f7009cfa5591a5f6e6a645c8359" args="(SimpleCo &)" -->
virtual int </td><td class="memItemRight" valign="bottom"><b>operator==</b> (<a class="el" href="classsc_1_1SimpleCo.html">SimpleCo</a> &)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="cbdc2cb2eceb8b72d4618e098980100f"></a><!-- doxytag: member="sc::SimpleCo::operator!=" ref="cbdc2cb2eceb8b72d4618e098980100f" args="(SimpleCo &u)" -->
int </td><td class="memItemRight" valign="bottom"><b>operator!=</b> (<a class="el" href="classsc_1_1SimpleCo.html">SimpleCo</a> &u)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="15fbd34105a0a2ca5acacad0bbb34f43"></a><!-- doxytag: member="sc::SimpleCo::force_constant" ref="15fbd34105a0a2ca5acacad0bbb34f43" args="(Ref< Molecule > &)" -->
double </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#15fbd34105a0a2ca5acacad0bbb34f43">force_constant</a> (<a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1Molecule.html">Molecule</a> > &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Returns an approximate force constant (a la Almlof). <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#3f1701a5bad283075e540472b907af34">update_value</a> (const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1Molecule.html">Molecule</a> > &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculates the value of the coordinate based on the geometry in the <a class="el" href="classsc_1_1Molecule.html" title="The Molecule class contains information about molecules.">Molecule</a>. <a href="#3f1701a5bad283075e540472b907af34"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="aa198230dec60562506f26d8deda8a8c"></a><!-- doxytag: member="sc::SimpleCo::bmat" ref="aa198230dec60562506f26d8deda8a8c" args="(const Ref< Molecule > &, RefSCVector &bmat, double coef=1.0)" -->
void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#aa198230dec60562506f26d8deda8a8c">bmat</a> (const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1Molecule.html">Molecule</a> > &, <a class="el" href="classsc_1_1RefSCVector.html">RefSCVector</a> &bmat, double coef=1.0)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill in a row of the B matrix. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="b1228f1ce77f2877e691f5881316c5dc"></a><!-- doxytag: member="sc::SimpleCo::calc_force_con" ref="b1228f1ce77f2877e691f5881316c5dc" args="(Molecule &)=0" -->
virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#b1228f1ce77f2877e691f5881316c5dc">calc_force_con</a> (<a class="el" href="classsc_1_1Molecule.html">Molecule</a> &)=0</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculates an approximate force constant and returns it's value. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#10b1ebd40ffbaf10deab875dcbc3a021">calc_intco</a> (<a class="el" href="classsc_1_1Molecule.html">Molecule</a> &, double *=0, double=1)=0</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the value of the coordinate based on what's in <a class="el" href="classsc_1_1Molecule.html" title="The Molecule class contains information about molecules.">Molecule</a>. <a href="#10b1ebd40ffbaf10deab875dcbc3a021"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="b3aa3352e10cf13dba404d67d303a040"></a><!-- doxytag: member="sc::SimpleCo::print_details" ref="b3aa3352e10cf13dba404d67d303a040" args="(const Ref< Molecule > &, std::ostream &=ExEnv::out0()) const " -->
void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#b3aa3352e10cf13dba404d67d303a040">print_details</a> (const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1Molecule.html">Molecule</a> > &, std::ostream &=ExEnv::out0()) const </td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Print the coordinate. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SimpleCo.html#ec8ebf037fefbf66718483c991d6ee98">equivalent</a> (<a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1IntCoor.html">IntCoor</a> > &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Tests to see if two coordinates are equivalent to each other. <a href="#ec8ebf037fefbf66718483c991d6ee98"></a><br></td></tr>
<tr><td colspan="2"><br><h2>Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="85cf2b0bf1664952a8feb2c950fb29d8"></a><!-- doxytag: member="sc::SimpleCo::natoms_" ref="85cf2b0bf1664952a8feb2c950fb29d8" args="" -->
int </td><td class="memItemRight" valign="bottom"><b>natoms_</b></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="423f0dec29c3e9cd5815bf0fc5cb79fa"></a><!-- doxytag: member="sc::SimpleCo::atoms" ref="423f0dec29c3e9cd5815bf0fc5cb79fa" args="" -->
int * </td><td class="memItemRight" valign="bottom"><b>atoms</b></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
The <a class="el" href="classsc_1_1SimpleCo.html" title="The SimpleCo abstract class describes a simple internal coordinate of a molecule...">SimpleCo</a> abstract class describes a simple internal coordinate of a molecule.
<p>
The number atoms involved can be 2, 3 or 4 and is determined by the specialization of <a class="el" href="classsc_1_1SimpleCo.html" title="The SimpleCo abstract class describes a simple internal coordinate of a molecule...">SimpleCo</a>.<p>
There are three ways to specify the atoms involved in the internal coordinate. The first way is a shorthand notation, just a vector of a label followed by the atom numbers (starting at 1) is given. For example, a stretch between two atoms, 1 and 2, is given, in the <a class="el" href="classsc_1_1ParsedKeyVal.html" title="Converts textual information into keyword/value assocations.">ParsedKeyVal</a> format, as <pre>
stretch<StreSimpleCo>: [ R12 1 2 ]
</pre><p>
The other two ways to specify the atoms are more general. With them, it is possible to give parameters for the <a class="el" href="classsc_1_1IntCoor.html" title="The IntCoor abstract class describes an internal coordinate of a molecule.">IntCoor</a> base class (and thus give the value of the coordinate). In the first of these input formats, a vector associated with the keyword atoms gives the atom numbers. The following specification for stretch is equivalent to that above: <pre>
stretch<StreSimpleCo>:( label = R12 atoms = [ 1 2 ] )
</pre><p>
In the second, a vector, atom_labels, is given along with a <a class="el" href="classsc_1_1Molecule.html" title="The Molecule class contains information about molecules.">Molecule</a> object. The atom labels are looked up in the <a class="el" href="classsc_1_1Molecule.html" title="The Molecule class contains information about molecules.">Molecule</a> object to find the atom numbers. The following specification for stretch is equivalent to those above: <pre>
molecule<Molecule>: (
{ atom_labels atoms geometry } = {
H1 H [ 1.0 0.0 0.0 ]
H2 H [-1.0 0.0 0.0 ] } )
stretch<StreSimpleCo>:( label = R12
atom_labels = [ H1 H2 ]
molecule = $:molecule )
</pre> <hr><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" name="586dd9e1bb276feb0b7d5d1535163156"></a><!-- doxytag: member="sc::SimpleCo::SimpleCo" ref="586dd9e1bb276feb0b7d5d1535163156" args="(int, const char *=0)" -->
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<td class="memname">sc::SimpleCo::SimpleCo </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname">, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char * </td>
<td class="paramname"> = <code>0</code></td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
This constructor takes an integer argument which is the number of atoms needed to describe the coordinate.
<p>
A second optional char* argument is a label for the coordinate. This argument is passed on to the <a class="el" href="classsc_1_1IntCoor.html" title="The IntCoor abstract class describes an internal coordinate of a molecule.">IntCoor</a> constructor.
</div>
</div><p>
<hr><h2>Member Function Documentation</h2>
<a class="anchor" name="10b1ebd40ffbaf10deab875dcbc3a021"></a><!-- doxytag: member="sc::SimpleCo::calc_intco" ref="10b1ebd40ffbaf10deab875dcbc3a021" args="(Molecule &, double *=0, double=1)=0" -->
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<td class="memname">virtual double sc::SimpleCo::calc_intco </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classsc_1_1Molecule.html">Molecule</a> & </td>
<td class="paramname">, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> = <code>0</code>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> = <code>1</code></td><td> </td>
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<td></td>
<td>)</td>
<td></td><td></td><td><code> [pure virtual]</code></td>
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<div class="memdoc">
<p>
Calculate the value of the coordinate based on what's in <a class="el" href="classsc_1_1Molecule.html" title="The Molecule class contains information about molecules.">Molecule</a>.
<p>
If given a double*, fill in that part of the B matrix. If the bmatrix is to be calculated, the third argument gives the coefficient.
</div>
</div><p>
<a class="anchor" name="ec8ebf037fefbf66718483c991d6ee98"></a><!-- doxytag: member="sc::SimpleCo::equivalent" ref="ec8ebf037fefbf66718483c991d6ee98" args="(Ref< IntCoor > &)" -->
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<td class="memname">int sc::SimpleCo::equivalent </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1IntCoor.html">IntCoor</a> > & </td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Tests to see if two coordinates are equivalent to each other.
<p>
This is false if the atoms don't match.
<p>Implements <a class="el" href="classsc_1_1IntCoor.html#257baf6ad2f5acbde08a53921889881d">sc::IntCoor</a>.</p>
</div>
</div><p>
<a class="anchor" name="e5d77a1e7645a1ed3e8e6f7141f3408c"></a><!-- doxytag: member="sc::SimpleCo::save_data_state" ref="e5d77a1e7645a1ed3e8e6f7141f3408c" args="(StateOut &)" -->
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<td class="memname">void sc::SimpleCo::save_data_state </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classsc_1_1StateOut.html">StateOut</a> & </td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<p>
Save the base classes (with save_data_state) and the members in the same order that the <a class="el" href="classsc_1_1StateIn.html" title="Restores objects that derive from SavableState.">StateIn</a> CTOR initializes them.
<p>
This must be implemented by the derived class if the class has data.
<p>Reimplemented from <a class="el" href="classsc_1_1IntCoor.html#948f573e29ca6a9a3d025547ced8a2b1">sc::IntCoor</a>.</p>
</div>
</div><p>
<a class="anchor" name="3f1701a5bad283075e540472b907af34"></a><!-- doxytag: member="sc::SimpleCo::update_value" ref="3f1701a5bad283075e540472b907af34" args="(const Ref< Molecule > &)" -->
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<td class="memname">void sc::SimpleCo::update_value </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1Molecule.html">Molecule</a> > & </td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
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<div class="memdoc">
<p>
Recalculates the value of the coordinate based on the geometry in the <a class="el" href="classsc_1_1Molecule.html" title="The Molecule class contains information about molecules.">Molecule</a>.
<p>
<p>Implements <a class="el" href="classsc_1_1IntCoor.html#8828313a2c5909e0338488ae4fb30785">sc::IntCoor</a>.</p>
</div>
</div><p>
<hr>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="simple_8h_source.html">simple.h</a></ul>
</div>
<hr>
<address>
<small>
Generated at Wed Oct 14 14:12:13 2009 for <a
href="http://www.mpqc.org">MPQC</a>
2.3.1 using the documentation package <a
href="http://www.doxygen.org">Doxygen</a>
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