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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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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include <iostream> |
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#include "types/MoleculeStamp.hpp" |
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|
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namespace oopse { |
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MoleculeStamp::MoleculeStamp() { |
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DefineParameter(Name, "name"); |
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deprecatedKeywords_.insert("nAtoms"); |
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deprecatedKeywords_.insert("nBonds"); |
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deprecatedKeywords_.insert("nBends"); |
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deprecatedKeywords_.insert("nTorsions"); |
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deprecatedKeywords_.insert("nRigidBodies"); |
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deprecatedKeywords_.insert("nCutoffGroups"); |
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} |
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|
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MoleculeStamp::~MoleculeStamp() { |
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|
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} |
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|
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bool MoleculeStamp::addAtomStamp( AtomStamp* atom) { |
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bool ret = addIndexSensitiveStamp(atomStamps_, atom); |
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if (!ret) { |
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std::cout << "multiple atoms have the same index: " << atom->getIndex() <<" in " << getName() << " Molecule\n"; |
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} |
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return ret; |
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} |
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|
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tim |
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bool MoleculeStamp::addBondStamp( BondStamp* bond) { |
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bondStamps_.push_back(bond); |
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return true; |
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} |
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bool MoleculeStamp::addBendStamp( BendStamp* bend) { |
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bendStamps_.push_back(bend); |
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return true; |
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} |
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|
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bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) { |
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torsionStamps_.push_back(torsion); |
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return true; |
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} |
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|
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bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) { |
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bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody); |
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if (!ret) { |
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std::cout << "multiple rigidbodies have the same index: " << rigidbody->getIndex() <<" in " << getName() << " Molecule\n"; |
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} |
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return ret; |
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} |
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|
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bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) { |
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cutoffGroupStamps_.push_back(cutoffgroup); |
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return true; |
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} |
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bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) { |
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return addIndexSensitiveStamp(fragmentStamps_, fragment); |
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} |
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void MoleculeStamp::validate() { |
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DataHolder::validate(); |
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std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL)); |
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if (ai != atomStamps_.end()) { |
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std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n"; |
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} |
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std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
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if (ri != rigidBodyStamps_.end()) { |
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std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
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} |
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|
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std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
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if (fi != fragmentStamps_.end()) { |
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std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
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} |
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//make sure index is not out of range |
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int natoms = getNAtoms(); |
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for(int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp = getBondStamp(i); |
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if (bondStamp->getA() >= natoms && bondStamp->getB() >= natoms) { |
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std::cout << "Error in Molecule " << getName() << ": bond between " << bondStamp->getA() << " and " << bondStamp->getB() << " is invalid\n"; |
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} |
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} |
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for(int i = 0; i < getNBends(); ++i) { |
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BendStamp* bendStamp = getBendStamp(i); |
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std::vector<int> bendAtoms = bendStamp->getMembers(); |
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std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1)); |
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if (j != bendAtoms.end()) { |
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std::cout << "Error in Molecule " << getName(); |
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} |
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if (bendAtoms.size() == 2 && !bendStamp->haveGhostVectorSource()) { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing"; |
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} |
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} |
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for(int i = 0; i < getNBends(); ++i) { |
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TorsionStamp* torsionStamp = getTorsionStamp(i); |
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std::vector<int> torsionAtoms = torsionStamp ->getMembers(); |
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std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1)); |
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if (j != torsionAtoms.end()) { |
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std::cout << "Error in Molecule " << getName(); |
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} |
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gezelter |
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} |
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for(int i = 0; i < getNCutoffGroups(); ++i) { |
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CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
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std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
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std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), natoms-1)); |
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if (j != cutoffGroupAtoms.end()) { |
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std::cout << "Error in Molecule " << getName(); |
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} |
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} |
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atom2Rigidbody.resize(natoms); |
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// negative number means atom is a free atom, does not belong to rigidbody |
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//every element in atom2Rigidbody has unique negative number at the very beginning |
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for(int i = 0; i < atom2Rigidbody.size(); ++i) { |
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atom2Rigidbody[i] = -1 - i; |
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} |
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for (int i = 0; i < getNRigidBodies(); ++i) { |
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RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
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std::vector<int> members = rbStamp->getMembers(); |
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for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) { |
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atom2Rigidbody[*j] = i; |
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} |
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} |
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//make sure atoms belong to same rigidbody do not bond to each other |
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for(int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp = getBondStamp(i); |
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if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) |
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std::cout << "Error in Molecule " << getName() << ": "<<"bond between " << bondStamp->getA() << " and " << bondStamp->getB() << "belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
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} |
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for(int i = 0; i < getNBends(); ++i) { |
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BendStamp* bendStamp = getBendStamp(i); |
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std::vector<int> bendAtoms = bendStamp->getMembers(); |
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std::vector<int> rigidSet(getNRigidBodies(), 0); |
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std::vector<int>::iterator j; |
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for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) { |
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int rigidbodyIndex = atom2Rigidbody[*j]; |
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if (rigidbodyIndex >= 0) { |
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++rigidSet[rigidbodyIndex]; |
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if (rigidSet[rigidbodyIndex] > 1) { |
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std::cout << "Error in Molecule " << getName() << ": "; |
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//std::cout << "atoms of bend " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
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} |
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} |
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} |
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} |
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for(int i = 0; i < getNTorsions(); ++i) { |
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TorsionStamp* torsionStamp = getTorsionStamp(i); |
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std::vector<int> torsionAtoms = torsionStamp->getMembers(); |
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std::vector<int> rigidSet(getNRigidBodies(), 0); |
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std::vector<int>::iterator j; |
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for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) { |
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int rigidbodyIndex = atom2Rigidbody[*j]; |
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if (rigidbodyIndex >= 0) { |
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++rigidSet[rigidbodyIndex]; |
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if (rigidSet[rigidbodyIndex] > 1) { |
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std::cout << "Error in Molecule " << getName() << ": "; |
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//std::cout << "atoms of torsion " << << "belong to same rigidbody " << rigidbodyIndex << "\n"; |
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} |
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} |
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} |
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} |
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//fill in bond information into atom |
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fillBondInfo(); |
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findBends(); |
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findTorsions(); |
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gezelter |
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|
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int nrigidAtoms = 0; |
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for (int i = 0; i < getNRigidBodies(); ++i) { |
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RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
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nrigidAtoms += rbStamp->getNMembers(); |
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} |
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nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms; |
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|
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} |
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|
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void MoleculeStamp::fillBondInfo() { |
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} |
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void MoleculeStamp::findBends() { |
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gezelter |
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} |
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tim |
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void MoleculeStamp::findTorsions() { |
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gezelter |
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|
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} |
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//Function Name: isBondInSameRigidBody |
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//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
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bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
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int rbA; |
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int rbB; |
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int consAtomA; |
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int consAtomB; |
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if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
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return false; |
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253 |
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if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
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return false; |
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256 |
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if(rbB == rbA) |
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return true; |
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else |
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return false; |
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} |
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// Function Name: isAtomInRigidBody |
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//return false if atom does not belong to a rigid body, otherwise return true |
264 |
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bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
265 |
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int whichRigidBody; |
266 |
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int consAtomIndex; |
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268 |
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return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex); |
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270 |
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} |
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272 |
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// Function Name: isAtomInRigidBody |
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//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
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//and consAtomIndex |
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//atomIndex : the index of atom in component |
276 |
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//whichRigidBody: the index of rigidbody in component |
277 |
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//consAtomIndex: the position of joint atom apears in rigidbody's definition |
278 |
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bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
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RigidBodyStamp* rbStamp; |
280 |
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int numRb; |
281 |
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int numAtom; |
282 |
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283 |
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whichRigidBody = -1; |
284 |
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consAtomIndex = -1; |
285 |
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286 |
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numRb = this->getNRigidBodies(); |
287 |
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288 |
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for(int i = 0 ; i < numRb; i++){ |
289 |
tim |
2469 |
rbStamp = this->getRigidBodyStamp(i); |
290 |
gezelter |
1490 |
numAtom = rbStamp->getNMembers(); |
291 |
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for(int j = 0; j < numAtom; j++) |
292 |
tim |
2469 |
if (rbStamp->getMemberAt(j) == atomIndex){ |
293 |
gezelter |
1490 |
whichRigidBody = i; |
294 |
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consAtomIndex = j; |
295 |
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return true; |
296 |
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} |
297 |
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} |
298 |
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299 |
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return false; |
300 |
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301 |
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} |
302 |
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303 |
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//return the position of joint atom apears in rigidbody's definition |
304 |
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//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
305 |
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//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
306 |
gezelter |
2204 |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
307 |
gezelter |
1490 |
RigidBodyStamp* rbStamp1; |
308 |
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RigidBodyStamp* rbStamp2; |
309 |
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int natomInRb1; |
310 |
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int natomInRb2; |
311 |
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int atomIndex1; |
312 |
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int atomIndex2; |
313 |
gezelter |
2204 |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
314 |
gezelter |
1490 |
|
315 |
tim |
2469 |
rbStamp1 = this->getRigidBodyStamp(rb1); |
316 |
gezelter |
1490 |
natomInRb1 =rbStamp1->getNMembers(); |
317 |
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318 |
tim |
2469 |
rbStamp2 = this->getRigidBodyStamp(rb2); |
319 |
gezelter |
1490 |
natomInRb2 =rbStamp2->getNMembers(); |
320 |
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321 |
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for(int i = 0; i < natomInRb1; i++){ |
322 |
tim |
2469 |
atomIndex1 = rbStamp1->getMemberAt(i); |
323 |
gezelter |
1490 |
|
324 |
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for(int j= 0; j < natomInRb1; j++){ |
325 |
tim |
2469 |
atomIndex2 = rbStamp2->getMemberAt(j); |
326 |
gezelter |
1490 |
|
327 |
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if(atomIndex1 == atomIndex2){ |
328 |
gezelter |
1930 |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
329 |
gezelter |
1490 |
break; |
330 |
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} |
331 |
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332 |
tim |
2469 |
} |
333 |
gezelter |
1490 |
|
334 |
tim |
2469 |
} |
335 |
gezelter |
1490 |
|
336 |
|
|
return jointAtomIndexPair; |
337 |
|
|
} |
338 |
tim |
2469 |
|
339 |
|
|
} |