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/dports/science/plumed/plumed2-2.7.2/src/tools/
H A DAtomNumber.h74 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) {
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H A DPDB.h49 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;
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H A DNeighborList.h44 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;
H A DNeighborList.cpp36 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()
H A DPDB.cpp135 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()
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/dports/science/plumed/plumed2-2.7.2/src/core/
H A DActionAtomistic.h47 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()
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H A DGenericMolInfo.h51 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 );
H A DActionWithVirtualAtom.h43 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()
H A DAtoms.h52 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()
H A DGenericMolInfo.cpp69 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()
H A DValue.cpp121 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()
H A DActionAtomistic.cpp61 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()
/dports/science/plumed/plumed2-2.7.2/src/reference/
H A DReferenceAtoms.h64 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()
H A DReferenceConfiguration.h81 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()
/dports/science/py-OpenMC/openmc-0.12.2/tests/unit_tests/
H A Dtest_deplete_atom_number.py14 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)
/dports/science/openmc/openmc-0.12.2/tests/unit_tests/
H A Dtest_deplete_atom_number.py14 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)
/dports/science/plumed/plumed2-2.7.2/src/multicolvar/
H A DMultiColvarBase.h106 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()
H A DBridgedMultiColvarFunction.h75 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()
/dports/science/plumed/plumed2-2.7.2/src/colvar/
H A DDimer.cpp148 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()
/dports/science/plumed/plumed2-2.7.2/src/analysis/
H A DDataCollectionObject.h42 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()
/dports/science/plumed/plumed2-2.7.2/src/generic/
H A DGroup.cpp151 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()
H A DFitToTemplate.cpp180 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()
H A DWholeMolecules.cpp108 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()
H A DDumpMassCharge.cpp133 vector<AtomNumber> atoms; in DumpMassCharge()
142 atoms.push_back(AtomNumber::index(i)); in DumpMassCharge()
176 requestAtoms(vector<AtomNumber>()); in prepare()
/dports/science/plumed/plumed2-2.7.2/src/adjmat/
H A DAdjacencyMatrixBase.h47 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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