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#ifndef _UTILITY_H_ |
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#define _UTILITY_H_ |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#ifndef UTILS_UTILITY_HPP |
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#define UTILS_UTILITY_HPP |
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#include <vector> |
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#include <math.h> |
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#include "config.h" |
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#include "utils/next_combination.hpp" |
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|
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using namespace std; |
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double dotProduct(vector<double>& v1, vector<double>& v2); |
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double norm2(vector<double>& x); |
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namespace OpenMD { |
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inline RealType roundMe( RealType x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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|
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/** |
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* @brief iteratively replace the sequence with wild cards |
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* @return true if more combination sequence is avaliable, otherwise |
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* return true |
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* @param cont iterator container, if expect the whole series of |
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* combinations, pass an empty iterator container. The user should |
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* not modify this iterator container |
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* @param sequence the whole sequence used to generate combination |
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* @param result a possible combination sequence which is set on return |
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* @param wildCard the wild card string. Its value is "X" by default |
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* @note since next_combination never returns an empty sequence, |
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* replaceWildCard will not generate one special combination, which |
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* is n identical wild cards (n is equal to the size of the passing |
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* sequence) |
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* |
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* @code |
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* vector<string> sv; |
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* vector<vector<string>::iterator> sic; |
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* vector<string> resultString; |
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* sv.push_back("H"); |
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* sv.push_back("C"); |
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* sv.push_back("N"); |
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|
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* while (replaceWithWildCard(sic, sv, resultString)) { |
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* for(vector<string>::iterator i = resultString.begin(); |
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* i != resultString.end(); ++i) { |
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* cout << *i << "\t"; |
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* } |
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* cout << endl; |
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* } |
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* //output |
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* //H X X |
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* //X C X |
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* //X X N |
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* //H C X |
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* //H X N |
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* //X C N |
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* //H C N |
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* @endcode |
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*/ |
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bool replaceWithWildCard(vector<vector<string>::iterator>& cont, |
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vector<string>& sequence, vector<string>& result, |
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const string& wildCard = "X"); |
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} |
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#endif |
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|
