/dports/science/plumed/plumed2-2.7.2/src/tools/ |
H A D | AtomNumber.h | 74 AtomNumber::AtomNumber() { in AtomNumber() function 79 AtomNumber::AtomNumber(unsigned i) { in AtomNumber() function 94 AtomNumber & AtomNumber::setSerial(unsigned i) { in setSerial() 102 AtomNumber & AtomNumber::setIndex(unsigned i) { in setIndex() 108 AtomNumber AtomNumber::serial(unsigned i) { in serial() 115 AtomNumber AtomNumber::index(unsigned i) { in index() 120 bool operator<(const AtomNumber&a,const AtomNumber&b) { 125 bool operator>(const AtomNumber&a,const AtomNumber&b) { 130 bool operator<=(const AtomNumber&a,const AtomNumber&b) { 135 bool operator>=(const AtomNumber&a,const AtomNumber&b) { [all …]
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H A D | PDB.h | 49 std::vector<AtomNumber> numbers; 50 std::map<AtomNumber,unsigned> number2index; 70 const std::vector<AtomNumber> & getAtomNumbers()const; 82 …void getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::stri… 88 std::string getAtomName(AtomNumber a) const; 90 unsigned getResidueNumber(AtomNumber a) const; 92 std::string getResidueName(AtomNumber a) const; 103 bool checkForAtom( AtomNumber a ) const ; 114 void setAtomNumbers( const std::vector<AtomNumber>& atoms ); 126 std::vector<AtomNumber> getAtomsInChain(const std::string& chainid)const; [all …]
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H A D | NeighborList.h | 44 std::vector<PLMD::AtomNumber> fullatomlist_,requestlist_; 56 NeighborList(const std::vector<PLMD::AtomNumber>& list0, 57 const std::vector<PLMD::AtomNumber>& list1, 61 NeighborList(const std::vector<PLMD::AtomNumber>& list0, 67 std::vector<PLMD::AtomNumber>& getFullAtomList(); 71 std::vector<PLMD::AtomNumber>& getReducedAtomList(); 89 std::pair<AtomNumber,AtomNumber> getClosePairAtomNumber(unsigned i) const;
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H A D | NeighborList.cpp | 36 NeighborList::NeighborList(const vector<AtomNumber>& list0, const vector<AtomNumber>& list1, in NeighborList() 59 NeighborList::NeighborList(const vector<AtomNumber>& list0, const bool& serial, const bool& do_pbc, in NeighborList() 79 vector<AtomNumber>& NeighborList::getFullAtomList() { in getFullAtomList() 177 vector<AtomNumber>& NeighborList::getReducedAtomList() { in getReducedAtomList() 180 AtomNumber index0=fullatomlist_[neighbors_[i].first]; in getReducedAtomList() 181 AtomNumber index1=fullatomlist_[neighbors_[i].second]; in getReducedAtomList() 211 pair<AtomNumber,AtomNumber> NeighborList::getClosePairAtomNumber(unsigned i) const { in getClosePairAtomNumber() 212 pair<AtomNumber,AtomNumber> Aneigh; in getClosePairAtomNumber() 213 …Aneigh=pair<AtomNumber,AtomNumber>(fullatomlist_[neighbors_[i].first],fullatomlist_[neighbors_[i].… in getClosePairAtomNumber()
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H A D | PDB.cpp | 135 void PDB::setAtomNumbers( const std::vector<AtomNumber>& atoms ) { in setAtomNumbers() 239 const std::vector<AtomNumber> & PDB::getAtomNumbers()const { in getAtomNumbers() 255 std::string PDB::getAtomName(AtomNumber a)const { in getAtomName() 264 unsigned PDB::getResidueNumber(AtomNumber a)const { in getResidueNumber() 273 std::string PDB::getResidueName(AtomNumber a) const { in getResidueName() 343 AtomNumber a; unsigned resno; in readFromFilepointer() 417 void PDB::getAtomRange( const std::string& chainname, AtomNumber& a_start, AtomNumber& a_end, std::… in getAtomRange() 472 std::vector<AtomNumber> tmp; in getAtomsInResidue() 484 std::vector<AtomNumber> tmp; in getAtomsInChain() 515 bool PDB::checkForAtom( AtomNumber a ) const { in checkForAtom() [all …]
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/dports/science/plumed/plumed2-2.7.2/src/core/ |
H A D | ActionAtomistic.h | 47 std::set<AtomNumber> unique; 49 std::set<AtomNumber> unique_local; 90 const Vector & getGlobalPosition(AtomNumber)const; 94 Vector & modifyGlobalPosition(AtomNumber); 105 Vector & modifyGlobalForce(AtomNumber); 139 AtomNumber getAbsoluteIndex(int i)const; 190 const std::set<AtomNumber> & getUnique()const; 191 const std::set<AtomNumber> & getUniqueLocal()const; 208 Vector & ActionAtomistic::modifyGlobalPosition(AtomNumber i) { in modifyGlobalPosition() 213 Vector & ActionAtomistic::modifyGlobalForce(AtomNumber i) { in modifyGlobalForce() [all …]
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H A D | GenericMolInfo.h | 51 std::vector< std::vector<AtomNumber> > read_backbone; 64 …tring>& resstrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone ); 65 std::string getAtomName(AtomNumber a)const; 66 bool checkForAtom(AtomNumber a)const; 67 unsigned getResidueNumber(AtomNumber a)const; 69 std::string getResidueName(AtomNumber a)const; 70 void interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms );
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H A D | ActionWithVirtualAtom.h | 43 AtomNumber index; 46 std::map<AtomNumber,Tensor> gradients; 56 void requestAtoms(const std::vector<AtomNumber> & a); 78 const std::map<AtomNumber,Tensor> & getGradients()const; 80 AtomNumber getIndex()const; 88 AtomNumber ActionWithVirtualAtom::getIndex()const { in getIndex() 113 const std::map<AtomNumber,Tensor> & ActionWithVirtualAtom::getGradients()const { in getGradients()
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H A D | Atoms.h | 52 std::set<AtomNumber> unique; 86 std::map<std::string,std::vector<AtomNumber> > groups; 142 void share(const std::set<AtomNumber>&); 222 AtomNumber addVirtualAtom(ActionWithVirtualAtom*); 224 ActionWithVirtualAtom* getVirtualAtomsAction(AtomNumber)const; 225 bool isVirtualAtom(AtomNumber)const; 226 void insertGroup(const std::string&name,const std::vector<AtomNumber>&a); 268 bool Atoms::isVirtualAtom(AtomNumber i)const { in isVirtualAtom() 273 ActionWithVirtualAtom* Atoms::getVirtualAtomsAction(AtomNumber i)const { in getVirtualAtomsAction()
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H A D | GenericMolInfo.cpp | 69 std::vector<AtomNumber> backbone; in GenericMolInfo() 92 AtomNumber astart,aend; in GenericMolInfo() 124 …tring>& restrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone ) { in getBackbone() 176 std::vector<AtomNumber> atomnumbers; in getBackbone() 202 void GenericMolInfo::interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms ) { in interpretSymbol() 242 atoms.push_back(AtomNumber::serial(n)); in interpretSymbol() 284 std::string GenericMolInfo::getAtomName(AtomNumber a)const { in getAtomName() 288 bool GenericMolInfo::checkForAtom(AtomNumber a)const { in checkForAtom() 292 unsigned GenericMolInfo::getResidueNumber(AtomNumber a)const { in getResidueNumber() 300 std::string GenericMolInfo::getResidueName(AtomNumber a)const { in getResidueName()
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H A D | Value.cpp | 121 AtomNumber an=aa->getAbsoluteIndex(j); in setGradients() 136 AtomNumber iatom=p.first; in setGradients() 145 const std::map<AtomNumber,Vector> & grad1(v1.gradients); in projection() 146 const std::map<AtomNumber,Vector> & grad2(v2.gradients); in projection() 148 AtomNumber a=p1.first; in projection()
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H A D | ActionAtomistic.cpp | 61 void ActionAtomistic::requestAtoms(const vector<AtomNumber> & a, const bool clearDep) { in requestAtoms() 153 void ActionAtomistic::parseAtomList(const std::string&key, std::vector<AtomNumber> &t) { in parseAtomList() 157 void ActionAtomistic::parseAtomList(const std::string&key,const int num, std::vector<AtomNumber> &t… in parseAtomList() 169 void ActionAtomistic::interpretAtomList( std::vector<std::string>& strings, std::vector<AtomNumber>… in interpretAtomList() 172 AtomNumber atom; in interpretAtomList() 181 for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i)); in interpretAtomList() 186 for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i)); in interpretAtomList() 191 vector<AtomNumber> atom_list; moldat->interpretSymbol( symbol, atom_list ); in interpretAtomList()
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/dports/science/plumed/plumed2-2.7.2/src/reference/ |
H A D | ReferenceAtoms.h | 64 std::vector<AtomNumber> indices; 71 void setAtomIndices( const std::vector<AtomNumber>& atomnumbers ); 83 void singleDomainRequests( std::vector<AtomNumber>&, bool disable_checks ); 93 void getAtomRequests( std::vector<AtomNumber>&, bool disable_checks=false ) override; 97 const std::vector<AtomNumber>& getAbsoluteIndexes() override; 156 const std::vector<AtomNumber>& ReferenceAtoms::getAbsoluteIndexes() { in getAbsoluteIndexes()
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H A D | ReferenceConfiguration.h | 81 std::vector<AtomNumber> fake_atom_numbers; 100 virtual void getAtomRequests( std::vector<AtomNumber>&, bool disable_checks=false ) {} 121 virtual const std::vector<AtomNumber>& getAbsoluteIndexes(); 153 const std::vector<AtomNumber>& ReferenceConfiguration::getAbsoluteIndexes() { in getAbsoluteIndexes()
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/dports/science/py-OpenMC/openmc-0.12.2/tests/unit_tests/ |
H A D | test_deplete_atom_number.py | 14 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 45 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 60 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 117 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 137 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2)
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/dports/science/openmc/openmc-0.12.2/tests/unit_tests/ |
H A D | test_deplete_atom_number.py | 14 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 45 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 60 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 117 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2) 137 number = atom_number.AtomNumber(local_mats, nuclides, volume, 2)
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/dports/science/plumed/plumed2-2.7.2/src/multicolvar/ |
H A D | MultiColvarBase.h | 106 void setupMultiColvarBase( const std::vector<AtomNumber>& atoms ); 135 bool parseMultiColvarAtomList(const std::string& key, const int& num, std::vector<AtomNumber>& t); 137 …void readAtomsLikeKeyword( const std::string & key, const int& natoms, std::vector<AtomNumber>& al… 139 …ring& key0, const std::string& key1, const std::string& key2, std::vector<AtomNumber>& all_atoms ); 142 … const bool& no_third_dim_accum, const bool& symmetric, std::vector<AtomNumber>& all_atoms ); 145 … const bool& allow2, const bool& no_third_dim_accum, std::vector<AtomNumber>& all_atoms ); 177 virtual AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned& i ) const ; 224 AtomNumber MultiColvarBase::getAbsoluteIndexOfCentralAtom( const unsigned& iatom ) const { in getAbsoluteIndexOfCentralAtom()
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H A D | BridgedMultiColvarFunction.h | 75 AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned& i ) const override; 77 const std::vector<AtomNumber> & getAbsoluteIndexes()const override; 96 const std::vector<AtomNumber> & BridgedMultiColvarFunction::getAbsoluteIndexes() const { in getAbsoluteIndexes() 131 AtomNumber BridgedMultiColvarFunction::getAbsoluteIndexOfCentralAtom(const unsigned& i) const { in getAbsoluteIndexOfCentralAtom()
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/dports/science/plumed/plumed2-2.7.2/src/colvar/ |
H A D | Dimer.cpp | 148 vector<AtomNumber> usedatoms1; 149 vector<AtomNumber> usedatoms2; 182 vector<AtomNumber> atoms; in Dimer() 210 AtomNumber ati; in Dimer() 224 AtomNumber ati; in Dimer() 232 AtomNumber atip2; in Dimer()
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/dports/science/plumed/plumed2-2.7.2/src/analysis/ |
H A D | DataCollectionObject.h | 42 std::vector<AtomNumber> indices; 49 …rsAndArgumentNames( const std::string& action_label, const std::vector<AtomNumber>& ind, const std… 55 Vector getAtomPosition( const AtomNumber& ind ) const ; 63 Vector DataCollectionObject::getAtomPosition( const AtomNumber& ind ) const { in getAtomPosition()
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/dports/science/plumed/plumed2-2.7.2/src/generic/ |
H A D | Group.cpp | 151 vector<AtomNumber> atoms; in Group() 178 AtomNumber at; Tools::convert(words[i],at); in Group() 186 std::vector<AtomNumber> remove; in Group() 189 std::vector<AtomNumber> notfound; in Group()
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H A D | FitToTemplate.cpp | 180 std::vector<AtomNumber> aligned; 308 Vector & ato (modifyGlobalPosition(AtomNumber::index(i))); in calculate() 317 Vector & ato (modifyGlobalPosition(AtomNumber::index(i))); in calculate() 331 totForce+=modifyGlobalForce(AtomNumber::index(i)); in apply() 342 Vector & f(modifyGlobalForce(AtomNumber::index(i))); in apply()
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H A D | WholeMolecules.cpp | 108 vector<vector<AtomNumber> > groups; 142 vector<AtomNumber> merge; in WholeMolecules() 144 vector<AtomNumber> group; in WholeMolecules() 174 std::vector< std::vector<AtomNumber> > backatoms; in WholeMolecules()
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H A D | DumpMassCharge.cpp | 133 vector<AtomNumber> atoms; in DumpMassCharge() 142 atoms.push_back(AtomNumber::index(i)); in DumpMassCharge() 176 requestAtoms(vector<AtomNumber>()); in prepare()
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/dports/science/plumed/plumed2-2.7.2/src/adjmat/ |
H A D | AdjacencyMatrixBase.h | 47 void finishMatrixSetup( const bool& symmetric, const std::vector<AtomNumber>& all_atoms ); 79 AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned& i ) const ; 94 AtomNumber AdjacencyMatrixBase::getAbsoluteIndexOfCentralAtom( const unsigned& iatom ) const { in getAbsoluteIndexOfCentralAtom()
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