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gezelter |
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/* |
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gezelter |
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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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tim |
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#include <algorithm> |
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tim |
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#include <functional> |
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gezelter |
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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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#include "utils/MemoryUtils.hpp" |
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namespace oopse { |
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|
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template<class ContainerType> |
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bool hasDuplicateElement(const ContainerType& cont) { |
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ContainerType tmp = cont; |
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std::sort(tmp.begin(), tmp.end()); |
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tmp.erase(std::unique(tmp.begin(), tmp.end()), tmp.end()); |
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return tmp.size() != cont.size(); |
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} |
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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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tim |
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MoleculeStamp::~MoleculeStamp() { |
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MemoryUtils::deletePointers(atomStamps_); |
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MemoryUtils::deletePointers(bondStamps_); |
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MemoryUtils::deletePointers(bendStamps_); |
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MemoryUtils::deletePointers(torsionStamps_); |
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MemoryUtils::deletePointers(rigidBodyStamps_); |
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MemoryUtils::deletePointers(cutoffGroupStamps_); |
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MemoryUtils::deletePointers(fragmentStamps_); |
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} |
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gezelter |
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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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tim |
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std::ostringstream oss; |
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oss<< "Error in Molecule " << getName() << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n"; |
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throw OOPSEException(oss.str()); |
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} |
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return ret; |
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} |
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gezelter |
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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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gezelter |
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|
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tim |
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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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gezelter |
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|
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tim |
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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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tim |
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std::ostringstream oss; |
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oss<< "Error in Molecule " << getName() << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\n"; |
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throw OOPSEException(oss.str()); |
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} |
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return ret; |
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} |
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gezelter |
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|
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tim |
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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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gezelter |
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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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gezelter |
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|
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tim |
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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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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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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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void MoleculeStamp::checkAtoms() { |
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tim |
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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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tim |
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std::ostringstream oss; |
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oss << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n"; |
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throw OOPSEException(oss.str()); |
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gezelter |
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} |
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tim |
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} |
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void MoleculeStamp::checkBonds() { |
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std::ostringstream oss; |
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tim |
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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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tim |
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if (bondStamp->getA() > natoms-1 || bondStamp->getA() < 0 || bondStamp->getB() > natoms-1 || bondStamp->getB() < 0 || bondStamp->getA() == bondStamp->getB()) { |
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oss << "Error in Molecule " << getName() << ": bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n"; |
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throw OOPSEException(oss.str()); |
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} |
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gezelter |
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} |
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tim |
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|
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tim |
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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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std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair); |
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if ( iter != allBonds.end()) { |
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tim |
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oss << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ") appears multiple times\n"; |
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throw OOPSEException(oss.str()); |
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tim |
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} else { |
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allBonds.insert(bondPair); |
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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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tim |
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oss << "Error in Molecule " << getName() << ": "<<"bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
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throw OOPSEException(oss.str()); |
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tim |
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} |
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} |
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} |
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void MoleculeStamp::checkBends() { |
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tim |
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std::ostringstream oss; |
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tim |
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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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tim |
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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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tim |
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std::vector<int>::iterator k =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::less<int>(), 0)); |
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if (j != bendAtoms.end() || k != bendAtoms.end()) { |
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oss << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << " have invalid indices\n"; |
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throw OOPSEException(oss.str()); |
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tim |
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} |
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tim |
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if (hasDuplicateElement(bendAtoms)) { |
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oss << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << " have duplicated indices\n"; |
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throw OOPSEException(oss.str()); |
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} |
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tim |
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if (bendAtoms.size() == 2 ) { |
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if (!bendStamp->haveGhostVectorSource()) { |
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tim |
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237 |
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oss << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n"; |
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throw OOPSEException(oss.str()); |
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tim |
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}else{ |
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int ghostIndex = bendStamp->getGhostVectorSource(); |
241 |
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if (ghostIndex < getNAtoms()) { |
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if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) { |
243 |
tim |
2544 |
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oss << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; |
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throw OOPSEException(oss.str()); |
246 |
tim |
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} |
247 |
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if (!getAtomStamp(ghostIndex)->haveOrientation()) { |
248 |
tim |
2544 |
|
249 |
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oss << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; |
250 |
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throw OOPSEException(oss.str()); |
251 |
tim |
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} |
252 |
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}else { |
253 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n"; |
254 |
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throw OOPSEException(oss.str()); |
255 |
tim |
2483 |
} |
256 |
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} |
257 |
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} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) { |
258 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; |
259 |
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throw OOPSEException(oss.str()); |
260 |
tim |
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} |
261 |
gezelter |
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} |
262 |
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263 |
tim |
2469 |
for(int i = 0; i < getNBends(); ++i) { |
264 |
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BendStamp* bendStamp = getBendStamp(i); |
265 |
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std::vector<int> bendAtoms = bendStamp->getMembers(); |
266 |
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std::vector<int> rigidSet(getNRigidBodies(), 0); |
267 |
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std::vector<int>::iterator j; |
268 |
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for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) { |
269 |
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int rigidbodyIndex = atom2Rigidbody[*j]; |
270 |
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if (rigidbodyIndex >= 0) { |
271 |
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++rigidSet[rigidbodyIndex]; |
272 |
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if (rigidSet[rigidbodyIndex] > 1) { |
273 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ": bend" << containerToString(bendAtoms) << " belong to same rigidbody " << rigidbodyIndex << "\n"; |
274 |
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throw OOPSEException(oss.str()); |
275 |
tim |
2469 |
} |
276 |
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} |
277 |
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} |
278 |
tim |
2483 |
} |
279 |
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280 |
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281 |
tim |
2507 |
std::set<IntTuple3> allBends; |
282 |
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std::set<IntTuple3>::iterator iter; |
283 |
tim |
2483 |
for(int i = 0; i < getNBends(); ++i) { |
284 |
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BendStamp* bendStamp= getBendStamp(i); |
285 |
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std::vector<int> bend = bendStamp->getMembers(); |
286 |
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if (bend.size() == 2) { |
287 |
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// in case we have two ghost bend. For example, |
288 |
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// bend { |
289 |
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// members (0, 1); |
290 |
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// ghostVectorSource = 0; |
291 |
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// } |
292 |
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// and |
293 |
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// bend { |
294 |
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// members (0, 1); |
295 |
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// ghostVectorSource = 0; |
296 |
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// } |
297 |
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// In order to distinguish them. we expand them to Tuple3. |
298 |
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// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1) |
299 |
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int ghostIndex = bendStamp->getGhostVectorSource(); |
300 |
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std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex); |
301 |
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if (j != bend.end()) { |
302 |
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bend.insert(j, ghostIndex); |
303 |
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} |
304 |
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} |
305 |
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306 |
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IntTuple3 bendTuple(bend[0], bend[1], bend[2]); |
307 |
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//make sure bendTuple.first is always less than or equal to bendTuple.third |
308 |
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if (bendTuple.first > bendTuple.third) { |
309 |
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std::swap(bendTuple.first, bendTuple.third); |
310 |
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} |
311 |
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312 |
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iter = allBends.find(bendTuple); |
313 |
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if ( iter != allBends.end()) { |
314 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ": " << "Bend" << containerToString(bend)<< " appears multiple times\n"; |
315 |
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throw OOPSEException(oss.str()); |
316 |
tim |
2483 |
} else { |
317 |
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allBends.insert(bendTuple); |
318 |
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} |
319 |
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} |
320 |
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321 |
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for (int i = 0; i < getNBonds(); ++i) { |
322 |
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BondStamp* bondStamp = getBondStamp(i); |
323 |
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int a = bondStamp->getA(); |
324 |
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int b = bondStamp->getB(); |
325 |
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326 |
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AtomStamp* atomA = getAtomStamp(a); |
327 |
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AtomStamp* atomB = getAtomStamp(b); |
328 |
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329 |
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//find bend c--a--b |
330 |
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AtomStamp::AtomIter ai; |
331 |
gezelter |
2543 |
for(int c= atomA->getFirstBondedAtom(ai);c != -1;c = atomA->getNextBondedAtom(ai)) |
332 |
tim |
2483 |
{ |
333 |
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if(b == c) |
334 |
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continue; |
335 |
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336 |
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IntTuple3 newBend(c, a, b); |
337 |
|
|
if (newBend.first > newBend.third) { |
338 |
|
|
std::swap(newBend.first, newBend.third); |
339 |
|
|
} |
340 |
|
|
|
341 |
|
|
if (allBends.find(newBend) == allBends.end() ) { |
342 |
|
|
allBends.insert(newBend); |
343 |
|
|
BendStamp * newBendStamp = new BendStamp(); |
344 |
|
|
newBendStamp->setMembers(newBend); |
345 |
|
|
addBendStamp(newBendStamp); |
346 |
|
|
} |
347 |
|
|
} |
348 |
|
|
|
349 |
|
|
//find bend a--b--c |
350 |
gezelter |
2543 |
for(int c= atomB->getFirstBondedAtom(ai);c != -1;c = atomB->getNextBondedAtom(ai)) |
351 |
tim |
2483 |
{ |
352 |
|
|
if(a == c) |
353 |
|
|
continue; |
354 |
|
|
|
355 |
|
|
IntTuple3 newBend( a, b, c); |
356 |
|
|
if (newBend.first > newBend.third) { |
357 |
|
|
std::swap(newBend.first, newBend.third); |
358 |
|
|
} |
359 |
|
|
if (allBends.find(newBend) == allBends.end() ) { |
360 |
|
|
allBends.insert(newBend); |
361 |
|
|
BendStamp * newBendStamp = new BendStamp(); |
362 |
|
|
newBendStamp->setMembers(newBend); |
363 |
|
|
addBendStamp(newBendStamp); |
364 |
|
|
} |
365 |
|
|
} |
366 |
|
|
} |
367 |
|
|
|
368 |
|
|
} |
369 |
|
|
|
370 |
|
|
void MoleculeStamp::checkTorsions() { |
371 |
tim |
2544 |
std::ostringstream oss; |
372 |
tim |
2493 |
for(int i = 0; i < getNTorsions(); ++i) { |
373 |
tim |
2485 |
TorsionStamp* torsionStamp = getTorsionStamp(i); |
374 |
|
|
std::vector<int> torsionAtoms = torsionStamp ->getMembers(); |
375 |
|
|
std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
376 |
tim |
2544 |
std::vector<int>::iterator k =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::less<int>(), 0)); |
377 |
|
|
|
378 |
|
|
if (j != torsionAtoms.end() || k != torsionAtoms.end()) { |
379 |
|
|
oss << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n"; |
380 |
|
|
throw OOPSEException(oss.str()); |
381 |
tim |
2485 |
} |
382 |
tim |
2544 |
if (hasDuplicateElement(torsionAtoms)) { |
383 |
|
|
oss << "Error in Molecule " << getName() << " : atoms of torsion" << containerToString(torsionAtoms) << " have duplicated indices\n"; |
384 |
|
|
throw OOPSEException(oss.str()); |
385 |
|
|
} |
386 |
tim |
2485 |
} |
387 |
|
|
|
388 |
tim |
2469 |
for(int i = 0; i < getNTorsions(); ++i) { |
389 |
|
|
TorsionStamp* torsionStamp = getTorsionStamp(i); |
390 |
|
|
std::vector<int> torsionAtoms = torsionStamp->getMembers(); |
391 |
|
|
std::vector<int> rigidSet(getNRigidBodies(), 0); |
392 |
|
|
std::vector<int>::iterator j; |
393 |
|
|
for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) { |
394 |
|
|
int rigidbodyIndex = atom2Rigidbody[*j]; |
395 |
|
|
if (rigidbodyIndex >= 0) { |
396 |
|
|
++rigidSet[rigidbodyIndex]; |
397 |
|
|
if (rigidSet[rigidbodyIndex] > 1) { |
398 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n"; |
399 |
|
|
throw OOPSEException(oss.str()); |
400 |
tim |
2469 |
} |
401 |
|
|
} |
402 |
|
|
} |
403 |
tim |
2483 |
} |
404 |
gezelter |
1490 |
|
405 |
tim |
2507 |
std::set<IntTuple4> allTorsions; |
406 |
|
|
std::set<IntTuple4>::iterator iter; |
407 |
tim |
2483 |
for(int i = 0; i < getNTorsions(); ++i) { |
408 |
|
|
TorsionStamp* torsionStamp= getTorsionStamp(i); |
409 |
|
|
std::vector<int> torsion = torsionStamp->getMembers(); |
410 |
|
|
if (torsion.size() == 3) { |
411 |
|
|
int ghostIndex = torsionStamp->getGhostVectorSource(); |
412 |
|
|
std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex); |
413 |
|
|
if (j != torsion.end()) { |
414 |
|
|
torsion.insert(j, ghostIndex); |
415 |
|
|
} |
416 |
|
|
} |
417 |
gezelter |
1490 |
|
418 |
tim |
2483 |
IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]); |
419 |
|
|
if (torsionTuple.first > torsionTuple.fourth) { |
420 |
|
|
std::swap(torsionTuple.first, torsionTuple.fourth); |
421 |
|
|
std::swap(torsionTuple.second, torsionTuple.third); |
422 |
|
|
} |
423 |
gezelter |
1490 |
|
424 |
tim |
2483 |
iter = allTorsions.find(torsionTuple); |
425 |
|
|
if ( iter == allTorsions.end()) { |
426 |
|
|
allTorsions.insert(torsionTuple); |
427 |
|
|
} else { |
428 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ": " << "Torsion" << containerToString(torsion)<< " appears multiple times\n"; |
429 |
|
|
throw OOPSEException(oss.str()); |
430 |
tim |
2483 |
} |
431 |
|
|
} |
432 |
|
|
|
433 |
|
|
for (int i = 0; i < getNBonds(); ++i) { |
434 |
|
|
BondStamp* bondStamp = getBondStamp(i); |
435 |
|
|
int b = bondStamp->getA(); |
436 |
|
|
int c = bondStamp->getB(); |
437 |
|
|
|
438 |
|
|
AtomStamp* atomB = getAtomStamp(b); |
439 |
|
|
AtomStamp* atomC = getAtomStamp(c); |
440 |
|
|
|
441 |
|
|
AtomStamp::AtomIter ai2; |
442 |
|
|
AtomStamp::AtomIter ai3; |
443 |
|
|
|
444 |
gezelter |
2543 |
for(int a = atomB->getFirstBondedAtom(ai2);a != -1;a = atomB->getNextBondedAtom(ai2)) |
445 |
tim |
2483 |
{ |
446 |
|
|
if(a == c) |
447 |
|
|
continue; |
448 |
|
|
|
449 |
gezelter |
2543 |
for(int d = atomC->getFirstBondedAtom(ai3);d != -1;d = atomC->getNextBondedAtom(ai3)) |
450 |
tim |
2483 |
{ |
451 |
|
|
if(d == b) |
452 |
|
|
continue; |
453 |
|
|
|
454 |
|
|
IntTuple4 newTorsion(a, b, c, d); |
455 |
|
|
//make sure the first element is always less than or equal to the fourth element in IntTuple4 |
456 |
|
|
if (newTorsion.first > newTorsion.fourth) { |
457 |
|
|
std::swap(newTorsion.first, newTorsion.fourth); |
458 |
|
|
std::swap(newTorsion.second, newTorsion.third); |
459 |
|
|
} |
460 |
|
|
if (allTorsions.find(newTorsion) == allTorsions.end() ) { |
461 |
|
|
allTorsions.insert(newTorsion); |
462 |
|
|
TorsionStamp * newTorsionStamp = new TorsionStamp(); |
463 |
|
|
newTorsionStamp->setMembers(newTorsion); |
464 |
|
|
addTorsionStamp(newTorsionStamp); |
465 |
|
|
} |
466 |
|
|
} |
467 |
|
|
} |
468 |
|
|
} |
469 |
|
|
|
470 |
|
|
} |
471 |
|
|
|
472 |
|
|
void MoleculeStamp::checkRigidBodies() { |
473 |
tim |
2544 |
std::ostringstream oss; |
474 |
tim |
2483 |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
475 |
|
|
if (ri != rigidBodyStamps_.end()) { |
476 |
tim |
2544 |
oss << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
477 |
|
|
throw OOPSEException(oss.str()); |
478 |
tim |
2483 |
} |
479 |
|
|
|
480 |
tim |
2469 |
for (int i = 0; i < getNRigidBodies(); ++i) { |
481 |
|
|
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
482 |
tim |
2483 |
std::vector<int> rigidAtoms = rbStamp ->getMembers(); |
483 |
|
|
std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
484 |
|
|
if (j != rigidAtoms.end()) { |
485 |
tim |
2544 |
oss << "Error in Molecule " << getName(); |
486 |
|
|
throw OOPSEException(oss.str()); |
487 |
tim |
2483 |
} |
488 |
|
|
|
489 |
|
|
} |
490 |
|
|
} |
491 |
gezelter |
1490 |
|
492 |
tim |
2483 |
void MoleculeStamp::checkCutoffGroups() { |
493 |
|
|
for(int i = 0; i < getNCutoffGroups(); ++i) { |
494 |
|
|
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
495 |
|
|
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
496 |
|
|
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
497 |
|
|
if (j != cutoffGroupAtoms.end()) { |
498 |
tim |
2544 |
std::ostringstream oss; |
499 |
|
|
oss << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; |
500 |
|
|
throw OOPSEException(oss.str()); |
501 |
tim |
2483 |
} |
502 |
|
|
} |
503 |
gezelter |
1490 |
} |
504 |
|
|
|
505 |
tim |
2483 |
void MoleculeStamp::checkFragments() { |
506 |
gezelter |
1490 |
|
507 |
tim |
2483 |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
508 |
|
|
if (fi != fragmentStamps_.end()) { |
509 |
tim |
2544 |
std::ostringstream oss; |
510 |
|
|
oss << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
511 |
|
|
throw OOPSEException(oss.str()); |
512 |
tim |
2483 |
} |
513 |
|
|
|
514 |
gezelter |
1490 |
} |
515 |
|
|
|
516 |
tim |
2483 |
void MoleculeStamp::fillBondInfo() { |
517 |
gezelter |
1490 |
|
518 |
tim |
2483 |
for (int i = 0; i < getNBonds(); ++i) { |
519 |
|
|
BondStamp* bondStamp = getBondStamp(i); |
520 |
|
|
int a = bondStamp->getA(); |
521 |
|
|
int b = bondStamp->getB(); |
522 |
|
|
AtomStamp* atomA = getAtomStamp(a); |
523 |
|
|
AtomStamp* atomB = getAtomStamp(b); |
524 |
|
|
atomA->addBond(i); |
525 |
|
|
atomA->addBondedAtom(b); |
526 |
|
|
atomB->addBond(i); |
527 |
|
|
atomB->addBondedAtom(a); |
528 |
|
|
|
529 |
|
|
} |
530 |
gezelter |
1490 |
} |
531 |
|
|
|
532 |
tim |
2483 |
|
533 |
|
|
|
534 |
gezelter |
1490 |
//Function Name: isBondInSameRigidBody |
535 |
|
|
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
536 |
|
|
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
537 |
|
|
int rbA; |
538 |
|
|
int rbB; |
539 |
|
|
int consAtomA; |
540 |
|
|
int consAtomB; |
541 |
|
|
|
542 |
|
|
if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
543 |
|
|
return false; |
544 |
|
|
|
545 |
|
|
if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
546 |
|
|
return false; |
547 |
|
|
|
548 |
|
|
if(rbB == rbA) |
549 |
|
|
return true; |
550 |
|
|
else |
551 |
|
|
return false; |
552 |
|
|
} |
553 |
|
|
|
554 |
|
|
// Function Name: isAtomInRigidBody |
555 |
|
|
//return false if atom does not belong to a rigid body, otherwise return true |
556 |
|
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
557 |
tim |
2485 |
return atom2Rigidbody[atomIndex] >=0 ; |
558 |
gezelter |
1490 |
|
559 |
|
|
} |
560 |
|
|
|
561 |
|
|
// Function Name: isAtomInRigidBody |
562 |
|
|
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
563 |
|
|
//and consAtomIndex |
564 |
|
|
//atomIndex : the index of atom in component |
565 |
|
|
//whichRigidBody: the index of rigidbody in component |
566 |
|
|
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
567 |
|
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
568 |
|
|
|
569 |
tim |
2485 |
|
570 |
|
|
|
571 |
gezelter |
1490 |
whichRigidBody = -1; |
572 |
|
|
consAtomIndex = -1; |
573 |
|
|
|
574 |
tim |
2485 |
if (atom2Rigidbody[atomIndex] >=0) { |
575 |
|
|
whichRigidBody = atom2Rigidbody[atomIndex]; |
576 |
|
|
RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody); |
577 |
|
|
int numAtom = rbStamp->getNMembers(); |
578 |
|
|
for(int j = 0; j < numAtom; j++) { |
579 |
tim |
2469 |
if (rbStamp->getMemberAt(j) == atomIndex){ |
580 |
gezelter |
1490 |
consAtomIndex = j; |
581 |
|
|
return true; |
582 |
|
|
} |
583 |
tim |
2485 |
} |
584 |
gezelter |
1490 |
} |
585 |
|
|
|
586 |
|
|
return false; |
587 |
|
|
|
588 |
|
|
} |
589 |
|
|
|
590 |
|
|
//return the position of joint atom apears in rigidbody's definition |
591 |
|
|
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
592 |
|
|
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
593 |
gezelter |
2204 |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
594 |
gezelter |
1490 |
RigidBodyStamp* rbStamp1; |
595 |
|
|
RigidBodyStamp* rbStamp2; |
596 |
|
|
int natomInRb1; |
597 |
|
|
int natomInRb2; |
598 |
|
|
int atomIndex1; |
599 |
|
|
int atomIndex2; |
600 |
gezelter |
2204 |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
601 |
gezelter |
1490 |
|
602 |
tim |
2469 |
rbStamp1 = this->getRigidBodyStamp(rb1); |
603 |
gezelter |
1490 |
natomInRb1 =rbStamp1->getNMembers(); |
604 |
|
|
|
605 |
tim |
2469 |
rbStamp2 = this->getRigidBodyStamp(rb2); |
606 |
gezelter |
1490 |
natomInRb2 =rbStamp2->getNMembers(); |
607 |
|
|
|
608 |
|
|
for(int i = 0; i < natomInRb1; i++){ |
609 |
tim |
2469 |
atomIndex1 = rbStamp1->getMemberAt(i); |
610 |
gezelter |
1490 |
|
611 |
|
|
for(int j= 0; j < natomInRb1; j++){ |
612 |
tim |
2469 |
atomIndex2 = rbStamp2->getMemberAt(j); |
613 |
gezelter |
1490 |
|
614 |
|
|
if(atomIndex1 == atomIndex2){ |
615 |
gezelter |
1930 |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
616 |
gezelter |
1490 |
break; |
617 |
|
|
} |
618 |
|
|
|
619 |
tim |
2469 |
} |
620 |
gezelter |
1490 |
|
621 |
tim |
2469 |
} |
622 |
gezelter |
1490 |
|
623 |
|
|
return jointAtomIndexPair; |
624 |
|
|
} |
625 |
tim |
2469 |
|
626 |
|
|
} |