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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 <functional> |
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#include <iostream> |
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#include <sstream> |
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#include "types/MoleculeStamp.hpp" |
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#include "utils/Tuple.hpp" |
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|
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namespace oopse { |
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|
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template<class ContainerType> |
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std::string containerToString(ContainerType& cont) { |
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std::ostringstream oss; |
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oss << "("; |
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typename ContainerType::iterator i = cont.begin(); |
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if (i != cont.end()) { |
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oss << *i; |
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++i; |
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} |
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for (; i != cont.end();++i) { |
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oss << ", "; |
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oss << *i; |
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} |
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oss << ")"; |
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return oss.str(); |
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} |
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|
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MoleculeStamp::MoleculeStamp() { |
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DefineParameter(Name, "name"); |
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|
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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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|
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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<< "Error in Molecule " << getName() << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n"; |
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} |
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return ret; |
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|
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} |
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|
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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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|
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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<< "Error in Molecule " << getName() << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\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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|
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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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|
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void MoleculeStamp::validate() { |
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DataHolder::validate(); |
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|
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atom2Rigidbody.resize(getNAtoms()); |
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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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|
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checkAtoms(); |
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checkBonds(); |
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fillBondInfo(); |
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checkBends(); |
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checkTorsions(); |
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checkRigidBodies(); |
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checkCutoffGroups(); |
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checkFragments(); |
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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::checkAtoms() { |
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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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|
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} |
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|
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void MoleculeStamp::checkBonds() { |
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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(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n"; |
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} |
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} |
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|
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//make sure bonds are unique |
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std::set<std::pair<int, int> > allBonds; |
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for(int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp= getBondStamp(i); |
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std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB()); |
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//make sure bondTuple.first is always less than or equal to bondTuple.third |
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if (bondPair.first > bondPair.second) { |
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std::swap(bondPair.first, bondPair.second); |
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} |
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|
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std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair); |
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if ( iter != allBonds.end()) { |
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std::cout << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ")appears multiple times\n"; |
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} else { |
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allBonds.insert(bondPair); |
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} |
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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(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
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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 MoleculeStamp::checkBends() { |
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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>(), getNAtoms()-1)); |
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if (j != bendAtoms.end()) { |
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std::cout << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << "have invalid indices\n"; |
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} |
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|
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if (bendAtoms.size() == 2 ) { |
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if (!bendStamp->haveGhostVectorSource()) { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n"; |
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}else{ |
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int ghostIndex = bendStamp->getGhostVectorSource(); |
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if (ghostIndex < getNAtoms()) { |
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if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; |
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} |
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if (!getAtomStamp(ghostIndex)->haveOrientation()) { |
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std::cout << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; |
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} |
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}else { |
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std::cout << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n"; |
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} |
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} |
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} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) { |
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std::cout << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; |
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} |
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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> 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() << ": bend" << containerToString(bendAtoms) << " 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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|
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|
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std::set<IntTuple3> allBends; |
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std::set<IntTuple3>::iterator iter; |
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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> bend = bendStamp->getMembers(); |
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if (bend.size() == 2) { |
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// in case we have two ghost bend. For example, |
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// bend { |
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// members (0, 1); |
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// ghostVectorSource = 0; |
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// } |
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// and |
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// bend { |
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// members (0, 1); |
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// ghostVectorSource = 0; |
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// } |
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// In order to distinguish them. we expand them to Tuple3. |
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// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1) |
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int ghostIndex = bendStamp->getGhostVectorSource(); |
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std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex); |
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if (j != bend.end()) { |
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bend.insert(j, ghostIndex); |
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} |
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} |
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|
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IntTuple3 bendTuple(bend[0], bend[1], bend[2]); |
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//make sure bendTuple.first is always less than or equal to bendTuple.third |
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if (bendTuple.first > bendTuple.third) { |
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std::swap(bendTuple.first, bendTuple.third); |
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} |
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|
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iter = allBends.find(bendTuple); |
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if ( iter != allBends.end()) { |
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std::cout << "Error in Molecule " << getName() << ": " << "Bend appears multiple times\n"; |
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} else { |
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allBends.insert(bendTuple); |
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} |
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} |
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|
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for (int i = 0; i < getNBonds(); ++i) { |
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BondStamp* bondStamp = getBondStamp(i); |
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int a = bondStamp->getA(); |
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int b = bondStamp->getB(); |
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|
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AtomStamp* atomA = getAtomStamp(a); |
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AtomStamp* atomB = getAtomStamp(b); |
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|
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//find bend c--a--b |
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AtomStamp::AtomIter ai; |
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for(int c= atomA->getFirstBonedAtom(ai);c != -1;c = atomA->getNextBonedAtom(ai)) |
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{ |
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if(b == c) |
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continue; |
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|
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IntTuple3 newBend(c, a, b); |
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if (newBend.first > newBend.third) { |
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std::swap(newBend.first, newBend.third); |
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} |
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|
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if (allBends.find(newBend) == allBends.end() ) { |
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allBends.insert(newBend); |
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BendStamp * newBendStamp = new BendStamp(); |
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newBendStamp->setMembers(newBend); |
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addBendStamp(newBendStamp); |
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} |
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} |
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|
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//find bend a--b--c |
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for(int c= atomB->getFirstBonedAtom(ai);c != -1;c = atomB->getNextBonedAtom(ai)) |
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{ |
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if(a == c) |
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continue; |
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|
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IntTuple3 newBend( a, b, c); |
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if (newBend.first > newBend.third) { |
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std::swap(newBend.first, newBend.third); |
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} |
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if (allBends.find(newBend) == allBends.end() ) { |
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allBends.insert(newBend); |
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BendStamp * newBendStamp = new BendStamp(); |
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newBendStamp->setMembers(newBend); |
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addBendStamp(newBendStamp); |
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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 MoleculeStamp::checkTorsions() { |
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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>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
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if (j != torsionAtoms.end()) { |
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std::cout << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n"; |
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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() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n"; |
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} |
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} |
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} |
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} |
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|
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std::set<IntTuple4> allTorsions; |
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std::set<IntTuple4>::iterator iter; |
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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> torsion = torsionStamp->getMembers(); |
| 371 |
if (torsion.size() == 3) { |
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int ghostIndex = torsionStamp->getGhostVectorSource(); |
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std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex); |
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if (j != torsion.end()) { |
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torsion.insert(j, ghostIndex); |
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} |
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} |
| 378 |
|
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IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]); |
| 380 |
if (torsionTuple.first > torsionTuple.fourth) { |
| 381 |
std::swap(torsionTuple.first, torsionTuple.fourth); |
| 382 |
std::swap(torsionTuple.second, torsionTuple.third); |
| 383 |
} |
| 384 |
|
| 385 |
iter = allTorsions.find(torsionTuple); |
| 386 |
if ( iter == allTorsions.end()) { |
| 387 |
allTorsions.insert(torsionTuple); |
| 388 |
} else { |
| 389 |
std::cout << "Error in Molecule " << getName() << ": " << "Torsion appears multiple times\n"; |
| 390 |
} |
| 391 |
} |
| 392 |
|
| 393 |
for (int i = 0; i < getNBonds(); ++i) { |
| 394 |
BondStamp* bondStamp = getBondStamp(i); |
| 395 |
int b = bondStamp->getA(); |
| 396 |
int c = bondStamp->getB(); |
| 397 |
|
| 398 |
AtomStamp* atomB = getAtomStamp(b); |
| 399 |
AtomStamp* atomC = getAtomStamp(c); |
| 400 |
|
| 401 |
AtomStamp::AtomIter ai2; |
| 402 |
AtomStamp::AtomIter ai3; |
| 403 |
|
| 404 |
for(int a = atomB->getFirstBonedAtom(ai2);a != -1;a = atomB->getNextBonedAtom(ai2)) |
| 405 |
{ |
| 406 |
if(a == c) |
| 407 |
continue; |
| 408 |
|
| 409 |
for(int d = atomC->getFirstBonedAtom(ai3);d != -1;d = atomC->getNextBonedAtom(ai3)) |
| 410 |
{ |
| 411 |
if(d == b) |
| 412 |
continue; |
| 413 |
|
| 414 |
IntTuple4 newTorsion(a, b, c, d); |
| 415 |
//make sure the first element is always less than or equal to the fourth element in IntTuple4 |
| 416 |
if (newTorsion.first > newTorsion.fourth) { |
| 417 |
std::swap(newTorsion.first, newTorsion.fourth); |
| 418 |
std::swap(newTorsion.second, newTorsion.third); |
| 419 |
} |
| 420 |
if (allTorsions.find(newTorsion) == allTorsions.end() ) { |
| 421 |
allTorsions.insert(newTorsion); |
| 422 |
TorsionStamp * newTorsionStamp = new TorsionStamp(); |
| 423 |
newTorsionStamp->setMembers(newTorsion); |
| 424 |
addTorsionStamp(newTorsionStamp); |
| 425 |
} |
| 426 |
} |
| 427 |
} |
| 428 |
} |
| 429 |
|
| 430 |
} |
| 431 |
|
| 432 |
void MoleculeStamp::checkRigidBodies() { |
| 433 |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
| 434 |
if (ri != rigidBodyStamps_.end()) { |
| 435 |
std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
| 436 |
} |
| 437 |
|
| 438 |
for (int i = 0; i < getNRigidBodies(); ++i) { |
| 439 |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
| 440 |
std::vector<int> rigidAtoms = rbStamp ->getMembers(); |
| 441 |
std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 442 |
if (j != rigidAtoms.end()) { |
| 443 |
std::cout << "Error in Molecule " << getName(); |
| 444 |
} |
| 445 |
|
| 446 |
} |
| 447 |
} |
| 448 |
|
| 449 |
void MoleculeStamp::checkCutoffGroups() { |
| 450 |
|
| 451 |
for(int i = 0; i < getNCutoffGroups(); ++i) { |
| 452 |
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
| 453 |
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
| 454 |
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 455 |
if (j != cutoffGroupAtoms.end()) { |
| 456 |
std::cout << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; |
| 457 |
} |
| 458 |
} |
| 459 |
} |
| 460 |
|
| 461 |
void MoleculeStamp::checkFragments() { |
| 462 |
|
| 463 |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
| 464 |
if (fi != fragmentStamps_.end()) { |
| 465 |
std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
| 466 |
} |
| 467 |
|
| 468 |
} |
| 469 |
|
| 470 |
void MoleculeStamp::fillBondInfo() { |
| 471 |
|
| 472 |
for (int i = 0; i < getNBonds(); ++i) { |
| 473 |
BondStamp* bondStamp = getBondStamp(i); |
| 474 |
int a = bondStamp->getA(); |
| 475 |
int b = bondStamp->getB(); |
| 476 |
AtomStamp* atomA = getAtomStamp(a); |
| 477 |
AtomStamp* atomB = getAtomStamp(b); |
| 478 |
atomA->addBond(i); |
| 479 |
atomA->addBondedAtom(b); |
| 480 |
atomB->addBond(i); |
| 481 |
atomB->addBondedAtom(a); |
| 482 |
|
| 483 |
} |
| 484 |
} |
| 485 |
|
| 486 |
|
| 487 |
|
| 488 |
//Function Name: isBondInSameRigidBody |
| 489 |
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
| 490 |
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
| 491 |
int rbA; |
| 492 |
int rbB; |
| 493 |
int consAtomA; |
| 494 |
int consAtomB; |
| 495 |
|
| 496 |
if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
| 497 |
return false; |
| 498 |
|
| 499 |
if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
| 500 |
return false; |
| 501 |
|
| 502 |
if(rbB == rbA) |
| 503 |
return true; |
| 504 |
else |
| 505 |
return false; |
| 506 |
} |
| 507 |
|
| 508 |
// Function Name: isAtomInRigidBody |
| 509 |
//return false if atom does not belong to a rigid body, otherwise return true |
| 510 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
| 511 |
return atom2Rigidbody[atomIndex] >=0 ; |
| 512 |
|
| 513 |
} |
| 514 |
|
| 515 |
// Function Name: isAtomInRigidBody |
| 516 |
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
| 517 |
//and consAtomIndex |
| 518 |
//atomIndex : the index of atom in component |
| 519 |
//whichRigidBody: the index of rigidbody in component |
| 520 |
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
| 521 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
| 522 |
|
| 523 |
|
| 524 |
|
| 525 |
whichRigidBody = -1; |
| 526 |
consAtomIndex = -1; |
| 527 |
|
| 528 |
if (atom2Rigidbody[atomIndex] >=0) { |
| 529 |
whichRigidBody = atom2Rigidbody[atomIndex]; |
| 530 |
RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody); |
| 531 |
int numAtom = rbStamp->getNMembers(); |
| 532 |
for(int j = 0; j < numAtom; j++) { |
| 533 |
if (rbStamp->getMemberAt(j) == atomIndex){ |
| 534 |
consAtomIndex = j; |
| 535 |
return true; |
| 536 |
} |
| 537 |
} |
| 538 |
} |
| 539 |
|
| 540 |
return false; |
| 541 |
|
| 542 |
} |
| 543 |
|
| 544 |
//return the position of joint atom apears in rigidbody's definition |
| 545 |
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
| 546 |
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
| 547 |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
| 548 |
RigidBodyStamp* rbStamp1; |
| 549 |
RigidBodyStamp* rbStamp2; |
| 550 |
int natomInRb1; |
| 551 |
int natomInRb2; |
| 552 |
int atomIndex1; |
| 553 |
int atomIndex2; |
| 554 |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
| 555 |
|
| 556 |
rbStamp1 = this->getRigidBodyStamp(rb1); |
| 557 |
natomInRb1 =rbStamp1->getNMembers(); |
| 558 |
|
| 559 |
rbStamp2 = this->getRigidBodyStamp(rb2); |
| 560 |
natomInRb2 =rbStamp2->getNMembers(); |
| 561 |
|
| 562 |
for(int i = 0; i < natomInRb1; i++){ |
| 563 |
atomIndex1 = rbStamp1->getMemberAt(i); |
| 564 |
|
| 565 |
for(int j= 0; j < natomInRb1; j++){ |
| 566 |
atomIndex2 = rbStamp2->getMemberAt(j); |
| 567 |
|
| 568 |
if(atomIndex1 == atomIndex2){ |
| 569 |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
| 570 |
break; |
| 571 |
} |
| 572 |
|
| 573 |
} |
| 574 |
|
| 575 |
} |
| 576 |
|
| 577 |
return jointAtomIndexPair; |
| 578 |
} |
| 579 |
|
| 580 |
} |
