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<div class="title">center_of_mass.cpp</div> </div>
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<a href="center__of__mass_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001
<a name="l00009"></a>00009 <span class="comment">// direct header</span>
<a name="l00010"></a>00010 <span class="preprocessor">#include "<a class="code" href="center__of__mass_8hpp.html" title="This file contains a class which defines represents a center of mass calculation based on coordinate ...">sample/center_of_mass.hpp</a>"</span>
<a name="l00011"></a>00011
<a name="l00012"></a>00012 <span class="comment">// other headers</span>
<a name="l00013"></a>00013 <span class="preprocessor">#include "../vendor/boost/numeric/bindings/traits/ublas_matrix.hpp"</span>
<a name="l00014"></a>00014 <span class="preprocessor">#include "../vendor/boost/numeric/bindings/lapack/gesvd.hpp"</span>
<a name="l00015"></a>00015 <span class="preprocessor">#include <boost/numeric/ublas/vector.hpp></span>
<a name="l00016"></a>00016 <span class="preprocessor">#include <boost/numeric/ublas/matrix.hpp></span>
<a name="l00017"></a>00017 <span class="preprocessor">#include <boost/numeric/ublas/lu.hpp></span>
<a name="l00018"></a>00018
<a name="l00019"></a>00019 <span class="preprocessor">#include "<a class="code" href="atoms_8hpp.html" title="This file contains a class which defines an atom group, i.e.">sample/atoms.hpp</a>"</span>
<a name="l00020"></a>00020 <span class="preprocessor">#include "<a class="code" href="atomselection_8hpp.html" title="This file contains a class which defines different types of atomselections.">sample/atomselection.hpp</a>"</span>
<a name="l00021"></a>00021 <span class="preprocessor">#include "<a class="code" href="coor3d_8hpp.html" title="This file contains definitions for coordinate vector types for different coordinate systems...">math/coor3d.hpp</a>"</span>
<a name="l00022"></a>00022 <span class="preprocessor">#include "<a class="code" href="coordinate__set_8hpp.html" title="This file contains a class which defines coordinates based on a coordinate system.">sample/coordinate_set.hpp</a>"</span>
<a name="l00023"></a>00023 <span class="preprocessor">#include "<a class="code" href="control_8hpp.html" title="This is a convenience header file which includes all essential header files from the control director...">control.hpp</a>"</span>
<a name="l00024"></a>00024 <span class="preprocessor">#include "log.hpp"</span>
<a name="l00025"></a>00025
<a name="l00026"></a>00026 <span class="keyword">using namespace </span>std;
<a name="l00027"></a>00027
<a name="l00028"></a>00028 <span class="comment">// code snippets for determinant are from http://www.anderswallin.net/</span>
<a name="l00029"></a>00029
<a name="l00030"></a><a class="code" href="center__of__mass_8cpp.html#a0c2659a7e8f10858738168465c2e9d85">00030</a> <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="center__of__mass_8cpp.html#a0c2659a7e8f10858738168465c2e9d85">determinant_sign</a>(<span class="keyword">const</span> boost::numeric::ublas::permutation_matrix<size_t>& pm)
<a name="l00031"></a>00031 {
<a name="l00032"></a>00032 <span class="keywordtype">int</span> pm_sign=1;
<a name="l00033"></a>00033 std::size_t size = pm.size();
<a name="l00034"></a>00034 <span class="keywordflow">for</span> (std::size_t i = 0; i < size; ++i)
<a name="l00035"></a>00035 <span class="keywordflow">if</span> (i != pm(i))
<a name="l00036"></a>00036 pm_sign *= -1.0; <span class="comment">// swap_rows would swap a pair of rows here, so we change sign</span>
<a name="l00037"></a>00037 <span class="keywordflow">return</span> pm_sign;
<a name="l00038"></a>00038 }
<a name="l00039"></a>00039
<a name="l00040"></a><a class="code" href="center__of__mass_8cpp.html#a05e78c32267b6a1b0500dc7bb54bf763">00040</a> <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="center__of__mass_8cpp.html#a05e78c32267b6a1b0500dc7bb54bf763">determinant</a>(boost::numeric::ublas::matrix<double>& m ) {
<a name="l00041"></a>00041 boost::numeric::ublas::permutation_matrix<size_t> pm(m.size1());
<a name="l00042"></a>00042 <span class="keywordtype">double</span> det = 1.0;
<a name="l00043"></a>00043 <span class="keywordflow">if</span>( boost::numeric::ublas::lu_factorize(m,pm) ) {
<a name="l00044"></a>00044 det = 0.0;
<a name="l00045"></a>00045 } <span class="keywordflow">else</span> {
<a name="l00046"></a>00046 <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> i = 0; i < m.size1(); i++)
<a name="l00047"></a>00047 det *= m(i,i); <span class="comment">// multiply by elements on diagonal</span>
<a name="l00048"></a>00048 det = det * <a class="code" href="center__of__mass_8cpp.html#a0c2659a7e8f10858738168465c2e9d85">determinant_sign</a>( pm );
<a name="l00049"></a>00049 }
<a name="l00050"></a>00050 <span class="keywordflow">return</span> det;
<a name="l00051"></a>00051 }
<a name="l00052"></a>00052
<a name="l00053"></a><a class="code" href="class_fit.html#a78d8df03c3e9f8aa6c8677a17b6a64cc">00053</a> <a class="code" href="class_fit.html#a78d8df03c3e9f8aa6c8677a17b6a64cc">Fit::Fit</a>(
<a name="l00054"></a>00054 <a class="code" href="class_atoms.html" title="Type class which represents a structure and manages atom selections.">Atoms</a>& atoms, <span class="comment">// contains IDs in sequence</span>
<a name="l00055"></a>00055 <a class="code" href="class_coordinate_set.html" title="A set of coordinates with an associated representation.">CoordinateSet</a>& cs, <span class="comment">// contains original coordinates of target</span>
<a name="l00056"></a>00056 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pcs_selection, <span class="comment">// selection corresponding to target</span>
<a name="l00057"></a>00057 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pcs_selection_manip, <span class="comment">// (sub-)selection of target which specifies which atoms to move</span>
<a name="l00058"></a>00058 <a class="code" href="class_coordinate_set.html" title="A set of coordinates with an associated representation.">CoordinateSet</a>& cs_ref, <span class="comment">// coordinate set of the reference structure</span>
<a name="l00059"></a>00059 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pref_selection ) <span class="comment">// selection correspoding to reference</span>
<a name="l00060"></a>00060 {
<a name="l00061"></a>00061 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>& cs_selection_manip = *pcs_selection_manip;
<a name="l00062"></a>00062 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>& ref_selection = *pref_selection;
<a name="l00063"></a>00063
<a name="l00064"></a>00064 <span class="comment">// since rotational fitting has some algorithmic complexity, we</span>
<a name="l00065"></a>00065 <span class="comment">// create a reduced copy for the target coordinate set to work with</span>
<a name="l00066"></a>00066 <span class="comment">// this makes things easier, i.e. we can neglect some mapping</span>
<a name="l00067"></a>00067
<a name="l00068"></a>00068 <a class="code" href="class_coordinate_set.html" title="A set of coordinates with an associated representation.">CoordinateSet</a> cs_redcopy(cs,pcs_selection,pref_selection);
<a name="l00069"></a>00069 <span class="keywordflow">if</span> (cs_redcopy.<a class="code" href="class_coordinate_set.html#a1ffa1a198ee81d3ed61bb52cae5f75a0">size</a>()!=cs_ref.<a class="code" href="class_coordinate_set.html#a1ffa1a198ee81d3ed61bb52cae5f75a0">size</a>()) {
<a name="l00070"></a>00070 <a class="code" href="class_err.html#a846c4a7446fbd3a2a462fd3a4be006a5">Err::Inst</a>()-><a class="code" href="class_err.html#abc356b3a463194ecfa4c77c54b0f3547">write</a>(<span class="stringliteral">"Fitting requires the reference and the target to contain the same number of atoms"</span>);
<a name="l00071"></a>00071 <span class="keywordflow">throw</span>;
<a name="l00072"></a>00072 }
<a name="l00073"></a>00073
<a name="l00074"></a>00074 <span class="comment">// pre-determine center of mass vectors for each coordinate set</span>
<a name="l00075"></a>00075 <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a> ref = <a class="code" href="class_center_of_mass.html" title="Helper class which takes Atoms and a Coordinate set and returns a cartesian coordinate.">CenterOfMass</a>(atoms,cs_ref,pref_selection);
<a name="l00076"></a>00076 <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a> pos = <a class="code" href="class_center_of_mass.html" title="Helper class which takes Atoms and a Coordinate set and returns a cartesian coordinate.">CenterOfMass</a>(atoms,cs_redcopy,pref_selection);
<a name="l00077"></a>00077
<a name="l00078"></a>00078 <span class="comment">// compute the correlation kernel</span>
<a name="l00079"></a>00079 <span class="keyword">using namespace </span>boost::numeric::ublas;
<a name="l00080"></a>00080
<a name="l00081"></a>00081 matrix<double> K = zero_matrix<double>(3, 3);
<a name="l00082"></a>00082 boost::numeric::ublas::vector<double> v(3);
<a name="l00083"></a>00083 boost::numeric::ublas::vector<double> u(3);
<a name="l00084"></a>00084 <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> i = 0; i < ref_selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>(); ++i)
<a name="l00085"></a>00085 {
<a name="l00086"></a>00086 <span class="keywordtype">size_t</span> index = ref_selection[i];
<a name="l00087"></a>00087 <span class="keywordtype">size_t</span> <span class="keywordtype">id</span> = atoms[index];
<a name="l00088"></a>00088 <span class="keywordtype">double</span> mi = <a class="code" href="class_database.html#a38f080e0e65850789ad4790b9ac38b01">Database::Inst</a>()-><a class="code" href="class_database.html#a682e1c9e6a74d078996ce787dd7fe8a1">masses</a>.<a class="code" href="class_database_masses_parameters.html#a4e5c04f9dd72e893f698e7dc19abbb3c">get</a>(<span class="keywordtype">id</span>);
<a name="l00089"></a>00089 v[0]=cs_redcopy.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i] - pos.<a class="code" href="class_cartesian_coor3_d.html#ab47a1ac36ff653f54d9fcda4cde8f1b6">x</a>;
<a name="l00090"></a>00090 v[1]=cs_redcopy.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i] - pos.<a class="code" href="class_cartesian_coor3_d.html#a58e2b98f1d69b8c440f022bda42b405a">y</a>;
<a name="l00091"></a>00091 v[2]=cs_redcopy.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i] - pos.<a class="code" href="class_cartesian_coor3_d.html#a078a39ffafebeb904e1c04cbc89181f0">z</a>;
<a name="l00092"></a>00092 u[0]=cs_ref.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i] - ref.<a class="code" href="class_cartesian_coor3_d.html#ab47a1ac36ff653f54d9fcda4cde8f1b6">x</a>;
<a name="l00093"></a>00093 u[1]=cs_ref.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i] - ref.<a class="code" href="class_cartesian_coor3_d.html#a58e2b98f1d69b8c440f022bda42b405a">y</a>;
<a name="l00094"></a>00094 u[2]=cs_ref.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i] - ref.<a class="code" href="class_cartesian_coor3_d.html#a078a39ffafebeb904e1c04cbc89181f0">z</a>;
<a name="l00095"></a>00095 cout << <span class="stringliteral">"ref, "</span> << cs_ref.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i] << <span class="stringliteral">", "</span> << cs_ref.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i] << <span class="stringliteral">", "</span> << cs_ref.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i] << endl;
<a name="l00096"></a>00096
<a name="l00097"></a>00097 K +=mi*outer_prod(u, v);
<a name="l00098"></a>00098 }
<a name="l00099"></a>00099 boost::numeric::ublas::matrix<double> U(3,3);
<a name="l00100"></a>00100 boost::numeric::ublas::matrix<double> Vt(3,3);
<a name="l00101"></a>00101 boost::numeric::ublas::vector<double> S(3);
<a name="l00102"></a>00102
<a name="l00103"></a>00103 <span class="comment">// do singular value decomposition for K</span>
<a name="l00104"></a>00104 <span class="comment">// boost::numeric::bindings::lapack::gesvd(K,S,U,Vt);</span>
<a name="l00105"></a>00105 <span class="comment">// U and Vt are swapped!</span>
<a name="l00106"></a>00106 boost::numeric::bindings::lapack::gesvd(K,S,Vt,U);
<a name="l00107"></a>00107
<a name="l00108"></a>00108 <span class="comment">// now the crucial information is contained in the determinant of the dot product between U and Vt</span>
<a name="l00109"></a>00109 boost::numeric::ublas::matrix<double> UVt = prod(U,Vt);
<a name="l00110"></a>00110 <span class="keywordtype">double</span> detUVt = <a class="code" href="center__of__mass_8cpp.html#a05e78c32267b6a1b0500dc7bb54bf763">determinant</a>(UVt);
<a name="l00111"></a>00111 boost::numeric::ublas::matrix<double> P = zero_matrix<double>(3,3);
<a name="l00112"></a>00112 P(0,0)=1;P(1,1)=1;P(2,2)=detUVt;
<a name="l00113"></a>00113 boost::numeric::ublas::matrix<double> PVt = prod(P,Vt);
<a name="l00114"></a>00114 boost::numeric::ublas::matrix<double> UPVt = prod( U , PVt );
<a name="l00115"></a>00115
<a name="l00116"></a>00116 <span class="comment">// UPVt is the rotation matrix, rotate & translate</span>
<a name="l00117"></a>00117 boost::numeric::ublas::vector<double> before(3);
<a name="l00118"></a>00118 boost::numeric::ublas::vector<double> after(3);
<a name="l00119"></a>00119 <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> i = 0; i < ref_selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>(); ++i)
<a name="l00120"></a>00120 {
<a name="l00121"></a>00121 before[0] = cs_redcopy.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i] - pos.<a class="code" href="class_cartesian_coor3_d.html#ab47a1ac36ff653f54d9fcda4cde8f1b6">x</a>;
<a name="l00122"></a>00122 before[1] = cs_redcopy.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i] - pos.<a class="code" href="class_cartesian_coor3_d.html#a58e2b98f1d69b8c440f022bda42b405a">y</a>;
<a name="l00123"></a>00123 before[2] = cs_redcopy.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i] - pos.<a class="code" href="class_cartesian_coor3_d.html#a078a39ffafebeb904e1c04cbc89181f0">z</a>;
<a name="l00124"></a>00124
<a name="l00125"></a>00125 cout << <span class="stringliteral">"in, "</span> << cs_redcopy.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i] << <span class="stringliteral">", "</span> << cs_redcopy.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i] << <span class="stringliteral">", "</span> << cs_redcopy.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i] << endl;
<a name="l00126"></a>00126
<a name="l00127"></a>00127 after = prod(UPVt,before);
<a name="l00128"></a>00128 cs_redcopy.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i]=after[0]+ref.<a class="code" href="class_cartesian_coor3_d.html#ab47a1ac36ff653f54d9fcda4cde8f1b6">x</a>;
<a name="l00129"></a>00129 cs_redcopy.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i]=after[1]+ref.<a class="code" href="class_cartesian_coor3_d.html#a58e2b98f1d69b8c440f022bda42b405a">y</a>;
<a name="l00130"></a>00130 cs_redcopy.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i]=after[2]+ref.<a class="code" href="class_cartesian_coor3_d.html#a078a39ffafebeb904e1c04cbc89181f0">z</a>;
<a name="l00131"></a>00131 }
<a name="l00132"></a>00132
<a name="l00133"></a>00133 <span class="comment">// now the coordinates are in the local copy, we need to map them back into the original coordinate set.</span>
<a name="l00134"></a>00134 <span class="keywordtype">size_t</span> csel_total = cs_selection_manip.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>();
<a name="l00135"></a>00135 <span class="keywordtype">size_t</span> ssel_total = ref_selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>();
<a name="l00136"></a>00136 <span class="keywordtype">size_t</span> csel_iter = 0; <span class="comment">// iterates target coordinate set</span>
<a name="l00137"></a>00137 <span class="keywordtype">size_t</span> ssel_iter = 0; <span class="comment">// iterates local copy</span>
<a name="l00138"></a>00138
<a name="l00139"></a>00139 <span class="keywordflow">while</span>( ( csel_iter < csel_total) && (ssel_iter < ssel_total) ) {
<a name="l00140"></a>00140 <span class="keywordtype">size_t</span> csel_index = cs_selection_manip[csel_iter];
<a name="l00141"></a>00141 <span class="keywordtype">size_t</span> ssel_index = ref_selection[ssel_iter];
<a name="l00142"></a>00142
<a name="l00143"></a>00143 <span class="keywordflow">if</span> (csel_index==ssel_index) {
<a name="l00144"></a>00144 cs.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[csel_index]=cs_redcopy.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[ssel_index];
<a name="l00145"></a>00145 cs.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[csel_index]=cs_redcopy.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[ssel_index];
<a name="l00146"></a>00146 cs.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[csel_index]=cs_redcopy.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[ssel_index];
<a name="l00147"></a>00147 cout << <span class="stringliteral">"out, "</span> << cs.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[csel_index] << <span class="stringliteral">", "</span> << cs.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[csel_index] << <span class="stringliteral">", "</span> << cs.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[csel_index] << endl;
<a name="l00148"></a>00148 ssel_iter++;
<a name="l00149"></a>00149 csel_iter++;
<a name="l00150"></a>00150 } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (csel_index>ssel_index) {
<a name="l00151"></a>00151 ssel_iter++;
<a name="l00152"></a>00152 } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (csel_index<ssel_index) {
<a name="l00153"></a>00153 csel_iter++;
<a name="l00154"></a>00154 }
<a name="l00155"></a>00155 }
<a name="l00156"></a>00156 <span class="comment">//done</span>
<a name="l00157"></a>00157 }
<a name="l00158"></a>00158
<a name="l00159"></a><a class="code" href="class_center_of_mass.html#ae1b3e949a1f523afa32acaf58f1dabfe">00159</a> <a class="code" href="class_center_of_mass.html#ae1b3e949a1f523afa32acaf58f1dabfe">CenterOfMass::CenterOfMass</a>(<a class="code" href="class_atoms.html" title="Type class which represents a structure and manages atom selections.">Atoms</a>& atoms,<a class="code" href="class_coordinate_set.html" title="A set of coordinates with an associated representation.">CoordinateSet</a>& cs, <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pcs_selection, <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pcofm_selection) {
<a name="l00160"></a>00160
<a name="l00161"></a>00161 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>& cs_selection = *pcs_selection;
<a name="l00162"></a>00162 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>& cofm_selection = *pcofm_selection;
<a name="l00163"></a>00163
<a name="l00164"></a>00164 <span class="keywordflow">if</span> (cs.<a class="code" href="class_coordinate_set.html#a7de7d0f33b5b3b0a1fea952d1507658a">get_representation</a>()!=<a class="code" href="coordinate__set_8hpp.html#a852a4456bfb79f5b8df21a570c7eeff8ad0f64430e58c5010eddd5289ab519800">CARTESIAN</a>) {
<a name="l00165"></a>00165 <a class="code" href="class_err.html#a846c4a7446fbd3a2a462fd3a4be006a5">Err::Inst</a>()-><a class="code" href="class_err.html#abc356b3a463194ecfa4c77c54b0f3547">write</a>(<span class="stringliteral">"Center of Mass only implementated for cartesian Coordinate Sets"</span>);
<a name="l00166"></a>00166 <span class="keywordflow">throw</span>;
<a name="l00167"></a>00167 }
<a name="l00168"></a>00168
<a name="l00169"></a>00169 <span class="keywordtype">size_t</span> csel_total = cs_selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>();
<a name="l00170"></a>00170 <span class="keywordtype">size_t</span> ssel_total = cofm_selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>();
<a name="l00171"></a>00171
<a name="l00172"></a>00172 <span class="keywordflow">if</span> (ssel_total<1) {
<a name="l00173"></a>00173 <a class="code" href="class_warn.html#ab06e92f8140f8f482c2acd6362ccc466">Warn::Inst</a>()-><a class="code" href="class_warn.html#adb03d0302a3ffad4267e4e13c659941b">write</a>(<span class="stringliteral">"Warning! Computing Center of Mass for an empty atomselection"</span>);
<a name="l00174"></a>00174 <a class="code" href="class_warn.html#ab06e92f8140f8f482c2acd6362ccc466">Warn::Inst</a>()-><a class="code" href="class_warn.html#adb03d0302a3ffad4267e4e13c659941b">write</a>(<span class="stringliteral">"Setting Center of mass to (0,0,0)"</span>);
<a name="l00175"></a>00175 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(0,0,0);
<a name="l00176"></a>00176 } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (csel_total<1) {
<a name="l00177"></a>00177 <a class="code" href="class_warn.html#ab06e92f8140f8f482c2acd6362ccc466">Warn::Inst</a>()-><a class="code" href="class_warn.html#adb03d0302a3ffad4267e4e13c659941b">write</a>(<span class="stringliteral">"Warning! Computing Center of Mass for an empty coordinate set"</span>);
<a name="l00178"></a>00178 <a class="code" href="class_warn.html#ab06e92f8140f8f482c2acd6362ccc466">Warn::Inst</a>()-><a class="code" href="class_warn.html#adb03d0302a3ffad4267e4e13c659941b">write</a>(<span class="stringliteral">"Setting Center of mass to (0,0,0)"</span>);
<a name="l00179"></a>00179 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(0,0,0);
<a name="l00180"></a>00180 } <span class="keywordflow">else</span> {
<a name="l00181"></a>00181
<a name="l00182"></a>00182 <a class="code" href="common_8hpp.html#a97e00498816de586c88eaba23df40296">coor2_t</a> xt,yt,zt;
<a name="l00183"></a>00183 <span class="keywordtype">double</span> m,mi;
<a name="l00184"></a>00184 xt = yt = zt = 0.0;
<a name="l00185"></a>00185 m = 0.0;
<a name="l00186"></a>00186
<a name="l00187"></a>00187 <span class="keywordtype">size_t</span> csel_iter = 0;
<a name="l00188"></a>00188 <span class="keywordtype">size_t</span> ssel_iter = 0;
<a name="l00189"></a>00189
<a name="l00190"></a>00190 <span class="keywordflow">while</span>( ( csel_iter < csel_total) && (ssel_iter < ssel_total) ) {
<a name="l00191"></a>00191 <span class="keywordtype">size_t</span> csel_index = cs_selection[csel_iter];
<a name="l00192"></a>00192 <span class="keywordtype">size_t</span> ssel_index = cofm_selection[ssel_iter];
<a name="l00193"></a>00193
<a name="l00194"></a>00194 <span class="keywordflow">if</span> (csel_index==ssel_index) {
<a name="l00195"></a>00195 <span class="keywordtype">size_t</span> csel_id = atoms[csel_index];
<a name="l00196"></a>00196 mi = <a class="code" href="class_database.html#a38f080e0e65850789ad4790b9ac38b01">Database::Inst</a>()-><a class="code" href="class_database.html#a682e1c9e6a74d078996ce787dd7fe8a1">masses</a>.<a class="code" href="class_database_masses_parameters.html#a4e5c04f9dd72e893f698e7dc19abbb3c">get</a>(csel_id);
<a name="l00197"></a>00197 m += mi;
<a name="l00198"></a>00198
<a name="l00199"></a>00199 xt += cs.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[csel_iter]*mi;
<a name="l00200"></a>00200 yt += cs.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[csel_iter]*mi;
<a name="l00201"></a>00201 zt += cs.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[csel_iter]*mi;
<a name="l00202"></a>00202
<a name="l00203"></a>00203 ssel_iter++;
<a name="l00204"></a>00204 csel_iter++;
<a name="l00205"></a>00205 } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (csel_index>ssel_index) {
<a name="l00206"></a>00206 ssel_iter++;
<a name="l00207"></a>00207 } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (csel_index<ssel_index) {
<a name="l00208"></a>00208 csel_iter++;
<a name="l00209"></a>00209 }
<a name="l00210"></a>00210 }
<a name="l00211"></a>00211
<a name="l00212"></a>00212 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(xt/m,yt/m,zt/m);
<a name="l00213"></a>00213
<a name="l00214"></a>00214 }
<a name="l00215"></a>00215
<a name="l00216"></a>00216 }
<a name="l00217"></a>00217
<a name="l00218"></a><a class="code" href="class_center_of_mass.html#a077da8a00d2b8c74eb11c63d0dd50315">00218</a> <a class="code" href="class_center_of_mass.html#ae1b3e949a1f523afa32acaf58f1dabfe">CenterOfMass::CenterOfMass</a>(<a class="code" href="class_atoms.html" title="Type class which represents a structure and manages atom selections.">Atoms</a>& atoms,<a class="code" href="class_frame.html" title="Stores Frame information and resembles the trajectory data.">Frame</a>& frame,<a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pselection) {
<a name="l00219"></a>00219
<a name="l00220"></a>00220 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>& selection = *pselection;
<a name="l00221"></a>00221
<a name="l00222"></a>00222 <span class="keywordflow">if</span> (selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>()==0) {
<a name="l00223"></a>00223 <a class="code" href="class_err.html#a846c4a7446fbd3a2a462fd3a4be006a5">Err::Inst</a>()-><a class="code" href="class_err.html#abc356b3a463194ecfa4c77c54b0f3547">write</a>(<span class="stringliteral">"Warning! Computing Center of Mass for an empty atomselection"</span>);
<a name="l00224"></a>00224 <a class="code" href="class_err.html#a846c4a7446fbd3a2a462fd3a4be006a5">Err::Inst</a>()-><a class="code" href="class_err.html#abc356b3a463194ecfa4c77c54b0f3547">write</a>(<span class="stringliteral">"Setting Center of mass to (0,0,0)"</span>);
<a name="l00225"></a>00225 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(0,0,0);
<a name="l00226"></a>00226 <span class="keywordflow">return</span>;
<a name="l00227"></a>00227 }
<a name="l00228"></a>00228
<a name="l00229"></a>00229 <a class="code" href="common_8hpp.html#a97e00498816de586c88eaba23df40296">coor2_t</a> xt,yt,zt;
<a name="l00230"></a>00230 <span class="keywordtype">double</span> m,mi;
<a name="l00231"></a>00231 xt = yt = zt = 0.0;
<a name="l00232"></a>00232 m = 0.0;
<a name="l00233"></a>00233
<a name="l00234"></a>00234 <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i=0;i<selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>();i++) {
<a name="l00235"></a>00235 <span class="keywordtype">size_t</span> sel_id = atoms[selection[i]];
<a name="l00236"></a>00236 mi = <a class="code" href="class_database.html#a38f080e0e65850789ad4790b9ac38b01">Database::Inst</a>()-><a class="code" href="class_database.html#a682e1c9e6a74d078996ce787dd7fe8a1">masses</a>.<a class="code" href="class_database_masses_parameters.html#a4e5c04f9dd72e893f698e7dc19abbb3c">get</a>(sel_id);
<a name="l00237"></a>00237 m += mi;
<a name="l00238"></a>00238 xt += frame.<a class="code" href="class_frame.html#a10a9ccdbc92e81bfe14563cd46ae8177">x</a>[selection[i]]*mi;
<a name="l00239"></a>00239 yt += frame.<a class="code" href="class_frame.html#a8671bc6ac76fe47a9ba23359c74df6a7">y</a>[selection[i]]*mi;
<a name="l00240"></a>00240 zt += frame.<a class="code" href="class_frame.html#aab6f6843f385567586e4466cc3d47c6a">z</a>[selection[i]]*mi;
<a name="l00241"></a>00241 }
<a name="l00242"></a>00242
<a name="l00243"></a>00243 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(xt/m,yt/m,zt/m);
<a name="l00244"></a>00244 }
<a name="l00245"></a>00245
<a name="l00246"></a>00246
<a name="l00247"></a><a class="code" href="class_center_of_mass.html#aab1f60162bace537d7b36d6a4d826caf">00247</a> <a class="code" href="class_center_of_mass.html#ae1b3e949a1f523afa32acaf58f1dabfe">CenterOfMass::CenterOfMass</a>(<a class="code" href="class_atoms.html" title="Type class which represents a structure and manages atom selections.">Atoms</a>& atoms,<a class="code" href="class_coordinate_set.html" title="A set of coordinates with an associated representation.">CoordinateSet</a>& cset,<a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>* pselection) {
<a name="l00248"></a>00248
<a name="l00249"></a>00249 <a class="code" href="class_i_atomselection.html" title="Interface for atom selections.">IAtomselection</a>& selection = *pselection;
<a name="l00250"></a>00250
<a name="l00251"></a>00251 <span class="keywordflow">if</span> (selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>()==0) {
<a name="l00252"></a>00252 <a class="code" href="class_err.html#a846c4a7446fbd3a2a462fd3a4be006a5">Err::Inst</a>()-><a class="code" href="class_err.html#abc356b3a463194ecfa4c77c54b0f3547">write</a>(<span class="stringliteral">"Warning! Computing Center of Mass for an empty atomselection"</span>);
<a name="l00253"></a>00253 <a class="code" href="class_err.html#a846c4a7446fbd3a2a462fd3a4be006a5">Err::Inst</a>()-><a class="code" href="class_err.html#abc356b3a463194ecfa4c77c54b0f3547">write</a>(<span class="stringliteral">"Setting Center of mass to (0,0,0)"</span>);
<a name="l00254"></a>00254 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(0,0,0);
<a name="l00255"></a>00255 <span class="keywordflow">return</span>;
<a name="l00256"></a>00256 }
<a name="l00257"></a>00257
<a name="l00258"></a>00258 <a class="code" href="common_8hpp.html#a97e00498816de586c88eaba23df40296">coor2_t</a> xt,yt,zt;
<a name="l00259"></a>00259 <span class="keywordtype">double</span> m,mi;
<a name="l00260"></a>00260 xt = yt = zt = 0.0;
<a name="l00261"></a>00261 m = 0.0;
<a name="l00262"></a>00262
<a name="l00263"></a>00263 <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i=0;i<selection.<a class="code" href="class_i_atomselection.html#ad225c0cf412aff0073b78895ed9c8ee1">size</a>();i++) {
<a name="l00264"></a>00264 <span class="keywordtype">size_t</span> sel_id = atoms[selection[i]];
<a name="l00265"></a>00265 mi = <a class="code" href="class_database.html#a38f080e0e65850789ad4790b9ac38b01">Database::Inst</a>()-><a class="code" href="class_database.html#a682e1c9e6a74d078996ce787dd7fe8a1">masses</a>.<a class="code" href="class_database_masses_parameters.html#a4e5c04f9dd72e893f698e7dc19abbb3c">get</a>(sel_id);
<a name="l00266"></a>00266 m += mi;
<a name="l00267"></a>00267 xt += cset.<a class="code" href="class_coordinate_set.html#a9779b8963cbe85bbadea1d591843346c">c1</a>[i]*mi;
<a name="l00268"></a>00268 yt += cset.<a class="code" href="class_coordinate_set.html#a9feb5f09ef294aec973250ce5ba10de6">c2</a>[i]*mi;
<a name="l00269"></a>00269 zt += cset.<a class="code" href="class_coordinate_set.html#aae9725d5ca213cb016fa2ad04c1d07f8">c3</a>[i]*mi;
<a name="l00270"></a>00270 }
<a name="l00271"></a>00271
<a name="l00272"></a>00272 m_center = <a class="code" href="class_cartesian_coor3_d.html" title="Type class which represents coordinates in cartesian space.">CartesianCoor3D</a>(xt/m,yt/m,zt/m);
<a name="l00273"></a>00273 }
<a name="l00274"></a>00274
<a name="l00275"></a><a class="code" href="class_center_of_mass.html#a039bcb3e3e582a44ac8fffb6a812ddcc">00275</a> <a class="code" href="class_center_of_mass.html#a039bcb3e3e582a44ac8fffb6a812ddcc">CenterOfMass::operator CartesianCoor3D</a>() {
<a name="l00276"></a>00276 <span class="keywordflow">return</span> m_center;
<a name="l00277"></a>00277 }
<a name="l00278"></a>00278
<a name="l00279"></a>00279 <span class="comment">// end of file</span>
</pre></div></div>
</div>
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