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#include "primitives/Molecule.hpp" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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#include "utils/ElementsTable.hpp" |
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#include "utils/StringUtils.hpp" |
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namespace OpenMD { |
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Molecule::Molecule(int stampId, int globalIndex, const std::string& molName, |
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int region) : stampId_(stampId), |
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int region) : |
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globalIndex_(globalIndex), |
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moleculeName_(molName), |
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region_(region), |
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stampId_(stampId), |
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region_(region), |
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moleculeName_(molName), |
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constrainTotalCharge_(false) { |
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} |
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// get the chain of base types for this atom type: |
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std::vector<AtomType*> ayb = at->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn = ayb[ayb.size()-1]->getName(); |
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std::string bn = UpperCase(ayb[ayb.size()-1]->getName()); |
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int obanum = etab.GetAtomicNum(bn.c_str()); |
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if (obanum != 0) { |
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RealType eneg = etab.GetElectroNeg(obanum); |
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if (eneg > 3.01) { |
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if (bn.compare("O")==0 || bn.compare("N")==0 |
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|| bn.compare("F")==0) |
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hBondAcceptors_.push_back( atom ); |
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} |
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} |
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} |
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// find electronegative atoms that are either bonded to hydrogens or are |
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// present in the same rigid bodies: |
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// find electronegative atoms that are either bonded to |
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// hydrogens or are present in the same rigid bodies: |
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for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) { |
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Atom* atom1 = bond->getAtomA(); |
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Atom* atom2 = bond->getAtomB(); |
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std::vector<AtomType*> ayb1 = at1->allYourBase(); |
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std::vector<AtomType*> ayb2 = at2->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
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std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
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int obanum1 = etab.GetAtomicNum(bn1.c_str()); |
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int obanum2 = etab.GetAtomicNum(bn2.c_str()); |
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|
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if (obanum1 == 1) { |
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if (obanum2 != 0) { |
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RealType eneg = etab.GetElectroNeg(obanum2); |
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if (eneg > 3.01) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom2; |
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donor->donatedHydrogen = atom1; |
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hBondDonors_.push_back( donor ); |
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} |
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} |
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} |
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if (obanum2 == 1) { |
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if (obanum1 != 0) { |
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RealType eneg = etab.GetElectroNeg(obanum1); |
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if (eneg > 3.01) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom1; |
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donor->donatedHydrogen = atom2; |
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hBondDonors_.push_back( donor ); |
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} |
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std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName()); |
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std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName()); |
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|
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if (bn1.compare("H")==0) { |
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if (bn2.compare("O")==0 || bn2.compare("N")==0 |
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|| bn2.compare("F")==0) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom2; |
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donor->donatedHydrogen = atom1; |
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hBondDonors_.push_back( donor ); |
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} |
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} |
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if (bn2.compare("H")==0) { |
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if (bn1.compare("O")==0 || bn1.compare("N")==0 |
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|| bn1.compare("F")==0) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom1; |
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donor->donatedHydrogen = atom2; |
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hBondDonors_.push_back( donor ); |
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} |
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} |
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} |
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|
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for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
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for(atom1 = rb->beginAtom(ai); atom1 != NULL; atom1 = rb->nextAtom(ai)) { |
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for (rb = beginRigidBody(rbIter); rb != NULL; |
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rb = nextRigidBody(rbIter)) { |
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for(atom1 = rb->beginAtom(ai); atom1 != NULL; |
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atom1 = rb->nextAtom(ai)) { |
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AtomType* at1 = atom1->getAtomType(); |
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// get the chain of base types for this atom type: |
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std::vector<AtomType*> ayb1 = at1->allYourBase(); |
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// use the last type in the chain of base types for the name: |
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std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
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int obanum1 = etab.GetAtomicNum(bn1.c_str()); |
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if (obanum1 != 0) { |
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RealType eneg = etab.GetElectroNeg(obanum1); |
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if (eneg > 3.01) { |
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for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
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atom2 = rb->nextAtom(aj)) { |
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AtomType* at2 = atom2->getAtomType(); |
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< |
// get the chain of base types for this atom type: |
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< |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
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< |
// use the last type in the chain of base types for the name: |
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std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
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int obanum2 = etab.GetAtomicNum(bn2.c_str()); |
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if (obanum2 == 1) { |
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HBondDonor* donor = new HBondDonor(); |
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donor->donorAtom = atom1; |
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< |
donor->donatedHydrogen = atom2; |
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< |
hBondDonors_.push_back( donor ); |
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} |
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> |
std::string bn1 = UpperCase(ayb1[ayb1.size()-1]->getName()); |
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> |
|
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> |
if (bn1.compare("O")==0 || bn1.compare("N")==0 |
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> |
|| bn1.compare("F")==0) { |
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> |
for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
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> |
atom2 = rb->nextAtom(aj)) { |
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> |
AtomType* at2 = atom2->getAtomType(); |
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> |
// get the chain of base types for this atom type: |
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> |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
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> |
// use the last type in the chain of base types for the name: |
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> |
std::string bn2 = UpperCase(ayb2[ayb2.size()-1]->getName()); |
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> |
if (bn2.compare("H")==0) { |
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> |
HBondDonor* donor = new HBondDonor(); |
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> |
donor->donorAtom = atom1; |
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> |
donor->donatedHydrogen = atom2; |
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> |
hBondDonors_.push_back( donor ); |
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} |
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} |
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} |
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} |
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< |
} |
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> |
} |
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} |
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< |
|
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> |
|
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RealType Molecule::getMass() { |
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StuntDouble* sd; |
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std::vector<StuntDouble*>::iterator i; |
