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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. 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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* 3. 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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|
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#include "io/ElectrostaticAtomTypesSectionParser.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "utils/NumericConstant.hpp" |
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namespace oopse { |
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|
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ElectrostaticAtomTypesSectionParser::ElectrostaticAtomTypesSectionParser() { |
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setSectionName("ElectrostaticAtomTypes"); |
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} |
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|
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void ElectrostaticAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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int nTokens = tokenizer.countTokens(); |
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|
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//in AtomTypeSection, a line at least contains 2 tokens |
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//atomTypeName and biggest rank |
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//for the time being, we only support up to quadrupole |
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// "name" must match the name in the AtomTypes section |
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// charge is given in units of electrons (1.61 x 10^-19 C) |
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// Directionality for dipoles and quadrupoles must be given because the body-fixed |
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// reference frame for directional atoms is determined by the *mass* distribution and |
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// not by the charge distribution. |
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// Dipoles are given in units of Debye |
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// Quadrupoles are given in units of |
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// name 0 charge |
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// name 1 charge |u| [theta phi psi] |
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// name 2 charge |u| Qxx Qyy Qzz [theta phi psi] |
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|
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if (nTokens < 2) { |
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std::cerr << "ElectrostaticAtomTypesSectionParser Error: Not enought Tokens at line " << lineNo << std::endl; |
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} else { |
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|
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std::string atomTypeName = tokenizer.nextToken(); |
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int biggestRank = tokenizer.nextTokenAsInt(); |
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nTokens -= 2; |
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|
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AtomType* atomType = ff.getAtomType(atomTypeName); |
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DirectionalAtomType* dAtomType; |
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if (atomType != NULL) { |
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|
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switch (biggestRank) { |
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case 0 : |
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parseCharge(tokenizer, atomType); |
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break; |
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|
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case 1 : |
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|
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dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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if (dAtomType == NULL) { |
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std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl; |
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} |
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|
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parseCharge(tokenizer, dAtomType); |
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parseDipole(tokenizer, dAtomType); |
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parseElectroBodyFrame(tokenizer, dAtomType); |
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break; |
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|
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case 2: |
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|
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dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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if (dAtomType == NULL) { |
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std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl; |
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} |
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|
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parseCharge(tokenizer, dAtomType); |
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parseDipole(tokenizer, dAtomType); |
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parseQuadruple(tokenizer, dAtomType); |
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parseElectroBodyFrame(tokenizer, dAtomType); |
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break; |
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|
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default : |
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break; |
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|
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} |
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|
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} else { |
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std::cerr << "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName |
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<< "at line " << lineNo << std::endl; |
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} |
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|
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} |
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|
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|
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} |
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|
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|
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void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer, |
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AtomType* atomType) { |
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|
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double charge = tokenizer.nextTokenAsDouble(); |
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|
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if (fabs(charge) > NumericConstant::epsilon) { |
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atomType->addProperty(new DoubleGenericData("Charge", charge)); |
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atomType->setCharge(); |
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} |
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} |
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void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer, |
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DirectionalAtomType* dAtomType) { |
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|
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double dipole = tokenizer.nextTokenAsDouble(); |
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|
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if (fabs(dipole) > NumericConstant::epsilon) { |
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|
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dAtomType->addProperty(new DoubleGenericData("Dipole", dipole)); |
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dAtomType->setDipole(); |
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} |
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} |
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|
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void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer, |
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DirectionalAtomType* dAtomType) { |
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|
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Vector3d Q; |
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Q[0] = tokenizer.nextTokenAsDouble(); |
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Q[1] = tokenizer.nextTokenAsDouble(); |
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Q[2] = tokenizer.nextTokenAsDouble(); |
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|
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if (fabs(Q[0]) > NumericConstant::epsilon && fabs(Q[1]) > NumericConstant::epsilon |
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&& fabs(Q[2]) > NumericConstant::epsilon) { |
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|
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dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q)); |
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dAtomType->setQuadrupole(); |
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} |
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} |
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void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer, |
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DirectionalAtomType* dAtomType) { |
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|
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double phi; |
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double theta; |
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double psi; |
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|
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if (tokenizer.countTokens() >=3 ) { |
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phi = tokenizer.nextTokenAsDouble()/180.0; |
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theta = tokenizer.nextTokenAsDouble()/180.0; |
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psi = tokenizer.nextTokenAsDouble()/180.0; |
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} else { |
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phi = 0.0; |
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theta = 0.0; |
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psi = 0.0; |
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} |
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|
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RotMat3x3d electroBodyFrame(phi, theta, psi); |
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dAtomType->setElectroBodyFrame(electroBodyFrame); |
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|
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} |
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|
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} //end namespace oopse |
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