Simpatico  v1.10
Simp::Species Member List

This is the complete list of members for Simp::Species, including all inherited members.

add(std::istream &in, const char *label, Type &value, bool isRequired=true)Util::ParamCompositeprotected
addBegin(const char *label)Util::ParamComposite
addBlank()Util::ParamComposite
addCArray(std::istream &in, const char *label, Type *value, int n, bool isRequired=true)Util::ParamCompositeprotected
addCArray2D(std::istream &in, const char *label, Type *value, int m, int n, int np, bool isRequired=true)Util::ParamCompositeprotected
addComponent(ParamComponent &param, bool isLeaf=true)Util::ParamCompositeprotected
addDArray(std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)Util::ParamCompositeprotected
addDMatrix(std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)Util::ParamCompositeprotected
addEnd()Util::ParamComposite
addFArray(std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)Util::ParamCompositeprotected
addParamComposite(ParamComposite &child, bool next=true)Util::ParamComposite
allocate()Simp::Speciesprotected
allocateAngles()Simp::Speciesprotected
allocateAtoms()Simp::Speciesprotected
allocateBonds()Simp::Speciesprotected
allocateDihedrals()Simp::Speciesprotected
AtomAngleIdArray typedefSimp::Species
atomAngleIds(int atomId) const Simp::Speciesinline
AtomBondIdArray typedefSimp::Species
atomBondIds(int atomId) const Simp::Speciesinline
AtomDihedralIdArray typedefSimp::Species
atomDihedralIds(int atomId) const Simp::Speciesinline
atomTypeId(int iAtom) const Simp::Speciesinline
atomTypeIds_Simp::Speciesprotected
capacity() const Simp::Speciesinline
className() const Util::ParamCompositeinline
clearCommunicator()Util::MpiFileIo
echo()Util::ParamComponentstatic
hasIoCommunicator() const Util::MpiFileIoinline
IArchive typedefUtil::Serializable
id() const Simp::Speciesinline
id_Simp::Speciesprotected
indent() const Util::ParamComponent
initializeAtomGroupIdArrays()Simp::Speciesprotected
initStatic()Util::ParamComponentstatic
ioCommunicator() const Util::MpiFileIoinline
isActive() const Util::ParamCompositeinline
isIoProcessor() const Util::MpiFileIoinline
isMutable() const Simp::Speciesinline
isRequired() const Util::ParamCompositeinline
isValid() const Simp::Species
load(Serializable::IArchive &ar)Util::ParamCompositevirtual
loadCArray(Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired)Util::ParamComposite
loadCArray(Serializable::IArchive &ar, const char *label, Type *value, int n)Util::ParamCompositeinline
loadCArray2D(Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired)Util::ParamComposite
loadCArray2D(Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np)Util::ParamComposite
loadDArray(Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)Util::ParamComposite
loadDArray(Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)Util::ParamCompositeinline
loadDMatrix(Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)Util::ParamComposite
loadDMatrix(Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)Util::ParamCompositeinline
loadDSymmMatrix(Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)Util::ParamComposite
loadDSymmMatrix(Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)Util::ParamCompositeinline
loadFArray(Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)Util::ParamComposite
loadFArray(Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)Util::ParamCompositeinline
loadOptional(Serializable::IArchive &ar)Util::ParamCompositevirtual
loadParamComposite(Serializable::IArchive &ar, ParamComposite &child, bool next=true)Util::ParamComposite
loadParamCompositeOptional(Serializable::IArchive &ar, ParamComposite &child, bool next=true)Util::ParamComposite
loadParameter(Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)Util::ParamComposite
loadParameter(Serializable::IArchive &ar, const char *label, Type &value)Util::ParamCompositeinline
loadParameters(Serializable::IArchive &ar)Simp::Speciesvirtual
loadSpeciesParam(Serializable::IArchive &ar)Simp::Speciesprotectedvirtual
makeAngle(int angleId, int atomId1, int atomId2, int atomId3, int angleType)Simp::Speciesprotected
makeBond(int bondId, int atomId1, int atomId2, int bondType)Simp::Speciesprotected
makeDihedral(int dihedralId, int atomId1, int atomId2, int atomId3, int atomId4, int dihedralType)Simp::Speciesprotected
matchStructure(std::istream &in)Simp::Species
MaxAnglePerAtomSimp::Speciesstatic
MaxBondPerAtomSimp::Speciesstatic
MaxDihedralPerAtomSimp::Speciesstatic
moleculeCapacity_Simp::Speciesprotected
MpiFileIo()Util::MpiFileIo
MpiFileIo(const MpiFileIo &other)Util::MpiFileIo
mutator()Simp::Speciesinline
nAngle() const Simp::Speciesinline
nAngle_Simp::Speciesprotected
nAtom() const Simp::Speciesinline
nAtom_Simp::Speciesprotected
nBond() const Simp::Speciesinline
nBond_Simp::Speciesprotected
nDihedral() const Simp::Speciesinline
nDihedral_Simp::Speciesprotected
NullIndexSimp::Speciesprotectedstatic
OArchive typedefUtil::Serializable
ParamComponent()Util::ParamComponentprotected
ParamComponent(const ParamComponent &other)Util::ParamComponentprotected
ParamComposite()Util::ParamComposite
ParamComposite(const ParamComposite &other)Util::ParamComposite
ParamComposite(int capacity)Util::ParamComposite
read(std::istream &in, const char *label, Type &value)Util::ParamComposite
readBegin(std::istream &in, const char *label, bool isRequired=true)Util::ParamComposite
readBlank(std::istream &in)Util::ParamComposite
readCArray(std::istream &in, const char *label, Type *value, int n)Util::ParamCompositeinline
readCArray2D(std::istream &in, const char *label, Type *value, int m, int n, int np)Util::ParamCompositeinline
readDArray(std::istream &in, const char *label, DArray< Type > &array, int n)Util::ParamCompositeinline
readDMatrix(std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)Util::ParamCompositeinline
readDSymmMatrix(std::istream &in, const char *label, DMatrix< Type > &matrix, int n)Util::ParamCompositeinline
readEnd(std::istream &in)Util::ParamComposite
readFArray(std::istream &in, const char *label, FArray< Type, N > &array)Util::ParamCompositeinline
readOptional(std::istream &in, const char *label, Type &value)Util::ParamCompositeinline
readOptionalCArray(std::istream &in, const char *label, Type *value, int n)Util::ParamCompositeinline
readOptionalCArray2D(std::istream &in, const char *label, Type *value, int m, int n, int np)Util::ParamCompositeinline
readOptionalDArray(std::istream &in, const char *label, DArray< Type > &array, int n)Util::ParamCompositeinline
readOptionalDMatrix(std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)Util::ParamCompositeinline
readOptionalDSymmMatrix(std::istream &in, const char *label, DMatrix< Type > &matrix, int n)Util::ParamCompositeinline
readOptionalFArray(std::istream &in, const char *label, FArray< Type, N > &array)Util::ParamCompositeinline
readParam(std::istream &in)Util::ParamCompositevirtual
readParamComposite(std::istream &in, ParamComposite &child, bool next=true)Util::ParamComposite
readParamCompositeOptional(std::istream &in, ParamComposite &child, bool next=true)Util::ParamComposite
readParameters(std::istream &in)Simp::Speciesvirtual
readParamOptional(std::istream &in)Util::ParamCompositevirtual
readSpeciesParam(std::istream &in)Simp::Speciesprotectedvirtual
readStructure(std::istream &in)Simp::Species
resetParam()Util::ParamCompositevirtual
save(Serializable::OArchive &ar)Simp::Speciesvirtual
saveOptional(Serializable::OArchive &ar)Util::ParamComposite
serialize(Archive &ar, const unsigned int version)Util::ParamComponent
setAtomType(int atomId, int atomType)Simp::Speciesprotected
setClassName(const char *className)Util::ParamCompositeprotected
setEcho(bool echo=true)Util::ParamComponentstatic
setId(int id)Simp::Species
setIndent(const ParamComponent &parent, bool next=true)Util::ParamComponent
setIoCommunicator(MPI::Intracomm &communicator)Util::MpiFileIo
setIsActive(bool isActive)Util::ParamCompositeprotected
setIsRequired(bool isRequired)Util::ParamCompositeprotected
setMutatorPtr(McMd::SpeciesMutator *mutatorPtr)Simp::Speciesprotected
setParent(ParamComponent &param, bool next=true)Util::ParamCompositeprotected
Species()Simp::Species
SpeciesAngle typedefSimp::Species
speciesAngle(int iAngle) const Simp::Speciesinline
speciesAngles_Simp::Speciesprotected
SpeciesBond typedefSimp::Species
speciesBond(int iBond) const Simp::Speciesinline
speciesBonds_Simp::Speciesprotected
speciesDihedral(int iDihedral) const Simp::Speciesinline
SpeciesDihedral typedefSimp::Species
speciesDihedrals_Simp::Speciesprotected
writeParam(std::ostream &out)Util::ParamCompositevirtual
writeStructure(std::ostream &out, std::string indent=std::string())Simp::Species
~ParamComponent()Util::ParamComponentvirtual
~ParamComposite()Util::ParamCompositevirtual
~Serializable()Util::Serializableinlinevirtual
~Species()Simp::Speciesvirtual
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