// Uncomment the following line to change the fontsize: // fontsize=14 ////////////////////////////////////////////////////////////////////////////////////////////// // Welcome to UMLet! // // Double-click on UML elements to add them to the diagram, or to copy them // Edit elements by modifying the text in this panel // Hold Ctrl to select multiple elements // Use Ctrl+mouse to select via lasso // // Use ± or Ctrl+mouse wheel to zoom // Drag a whole relation at its central square icon // // Press Ctrl+C to copy the whole diagram to the system clipboard (then just paste it to, eg, Word) // Edit the files in the "palettes" directory to create your own element palettes // // Select "Custom Elements > New..." to create new element types ////////////////////////////////////////////////////////////////////////////////////////////// // This text will be stored with each diagram; use it for notes.7com.umlet.element.base.Class185529414770AtomInfo -- -x,v,F: Vector element *type; //!< pointing to element -- #AtomInfo(); #~AtomInfo(); com.umlet.element.base.Relation164531522334lt=<<<<-210;21;21;21com.umlet.element.base.Class1274147392259Element -- mass: double CovalentRadius: double VanDerWaalsRadius: double Z: int name: char[64] symbol: char[3] period: char[8] group: char[8] block: char[8] sort: int * No: int Valence: double NoValenceOrbitals: int HBondDistance: double[NDIM] HBondAngle: double[NDIM] -- #element(); #~element(); #Output(ofstream * const out) const: bool #Checkout(ofstream * const out, const int No, const int NoOfAtoms) const: boolcom.umlet.element.base.Class1960532280161BondedParticle -- -- #Operation(i: int): int #BondedParticle() /+virtual ~BondedParticle()/ #RegisterBond(bond *Binder): bool #UnregisterBond(bond *Binder): bool #IsBondedTo(BondedParticle * const BondPartner): bool #UnregisterAllBond(); #CountBonds() const: int #CorrectBondDegree(): int #OutputBondOfAtom() const #OutputAdjacency(ofstream *AdjacencyFile) const #OutputOrder(ofstream *file) constcom.umlet.element.base.Relation2184343258202lt=<<-245;21;245;154;21;154;21;189com.umlet.element.base.Relation1925343293202lt=<<- 21;21;21;154;280;154;280;189com.umlet.element.base.Relation218434334202lt=<<-21;21;21;189com.umlet.element.base.Class235929414770BondedParticleInfo -- AdaptiveOrder: unsigned char MaxOrder: bool -- #BondedParticleInfo() #~BondedParticleInfo() com.umlet.element.base.Class207928021784ParticleInfo -- nr: int Name: char * -- #ParticleInfo() #~ParticleInfo() #ostream & operator << (ostream &ost) const com.umlet.element.base.Relation248531517434lt=<<<<-21;21;161;21com.umlet.element.base.Class2646245147133BondList {Some Properties} -- -id: Long _-ClassAttribute: Long_ -- #Operation(i: int): int /+AbstractOperation()/ -- Responsibilities -- Resp1 *-- Resp2*com.umlet.element.base.Class1372427147105GraphNodeInfo -- -- GraphNr: int ComponentNr: int * LowpointNr: int SeparationVertex: bool IsCyclic: bool -- #GraphNodeInfo() #~GraphNodeInfo() com.umlet.element.base.Class148460912670GraphNode -- -- #GraphNode() /+~GraphNode()/ #OutputGraphInfo() const #OutputComponentNumber() const com.umlet.element.base.Relation1484343748279lt=<<-735;21;735;70;217;70;217;210;21;210;21;266com.umlet.element.base.Relation148451134111lt=<<-21;21;21;98com.umlet.element.base.Class1288756588245Atom -- sort: int* -- #atom() #atom(class atom *pointer) /+~atom()/ #OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const: bool #OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const: bool #OutputXYZLine(ofstream *out) const: bool #OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const: bool #OutputTrajectoryXYZ(ofstream * const out, const int step) const: bool #OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const #InitComponentNr() #EqualsFather ( const atom *ptr, const atom **res ) const #CorrectFather() #GetTrueFather(): atom * #Compare(const atom &ptr) const: bool #DistanceToVector(const Vector &origin) const: double #DistanceSquaredToVector(const Vector &origin) const: double #IsInParallelepiped(const Vector offset, const double *parallelepiped) const: boolcom.umlet.element.base.Relation137951183258lt=<<<<-21;21;21;182;70;182;70;245com.umlet.element.base.Class2226749504210TrajectoryParticle -- -- #TrajectoryParticle() /+~TrajectoryParticle()/ #AddKineticToTemperature(double *temperature, int step) const #EvaluateConstrainedForce(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force) const #CorrectVelocity(double *ActualTemp, int Step, Vector *CoGVelocity) #ResizeTrajectory(int MaxSteps) #CopyStepOnStep(int dest, int src) #VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force) #SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const #Thermostat_Woodcock(double ScaleTempFactor, int Step, double *ekin) #Thermostat_Gaussian_init(int Step, double *G, double *E) #Thermostat_Gaussian_least_constraint(int Step, double G_over_E, double *ekin, config *configuration) #Thermostat_Langevin(int Step, gsl_rng * r, double *ekin, config *configuration) #Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration) #Thermostat_NoseHoover_init(int Step, double *delta_alpha) #Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)com.umlet.element.base.Relation2149343209419lt=<<-21;21;21;112;196;112;196;406com.umlet.element.base.Relation1967343391419lt=<<-21;21;21;112;378;112;378;406com.umlet.element.base.Class161757420370TrajectoryParticleInfo -- Trajectory: struct {vector<Vector> R,U,V} FixedIon: int -- #TrajectoryParticleInfo() #~TrajectoryParticleInfo()com.umlet.element.base.Relation1757623601139lt=<<-21;21;21;105;588;105;588;126com.umlet.element.base.Relation172962334146lt=<<-21;21;21;133com.umlet.element.base.Relation1519658244111lt=<<-21;21;21;56;231;56;231;98com.umlet.element.base.Class1736448147112TesselPoint -- -id: Long _-ClassAttribute: Long_ -- #Operation(i: int): int /+AbstractOperation()/ -- Responsibilities -- Resp1 *-- Resp2*com.umlet.element.base.Relation1729539146230lt=<<-133;21;133;175;21;175;21;217com.umlet.element.base.Relation172967239897lt=<<-385;21;385;42;21;42;21;84com.umlet.element.base.Relation1729343398426lt=<<-385;21;385;168;196;168;196;371;21;371;21;413com.umlet.element.base.Relation1729343209426lt=<<-196;21;196;371;21;371;21;413com.umlet.element.base.Class833854357224Bond -- HydrogenBond: int BondDegree: int nr: int Cyclic: bool Type: enum EdgeType Used: enum Shading -- #GetOtherAtom(const ParticleInfo * const Atom) const: atom * #MarkUsed(const enum Shading color): bool #IsUsed(): enum Shading #ResetUsed() #Contains(const ParticleInfo * const ptr): bool #Contains(const int nr): bool #GetDistance() const: double #GetDistanceSquared() const: double #bond() #bond(atom *left, atom *right, const int degree=1, const int number=0) #~bond()com.umlet.element.base.Relation1834707107125lt=<<<<- 342;112;91;112;91;35;21;35;21;49com.umlet.element.base.Relation116989613249lt=<<<<- 221;35;119;35com.umlet.element.base.Relation770742111167lt=<<<<- 263;154;28;154;28;35;98;35;98;112com.umlet.element.base.Class11131330504168BondGraph -- max_distance: double IsAngstroem: bool -- #BondGraph(bool IsA); #~BondGraph(); #LoadBondLengthTable(const string &filename): bool #ConstructBondGraph(molecule * const mol): bool #GetBondLength(int firstelement, int secondelement): double #SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol): double #BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem) #CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)com.umlet.element.base.Relation1596140716734lt=<<<<-21;21;154;21com.umlet.element.base.Class17501365147133MatrixContainer -- -id: Long _-ClassAttribute: Long_ -- #Operation(i: int): int /+AbstractOperation()/ -- Responsibilities -- Resp1 *-- Resp2*com.umlet.element.base.Class05395111050config -- PsiType: int MaxPsiDouble: int PsiMaxNoUp: int PsiMaxNoDown: int MaxMinStopStep: int InitMaxMinStopStep: int ProcPEGamma: int ProcPEPsi: int configpath: char * configname: char * FastParsing: bool Deltat: double basis: string databasepath: char * DoConstrainedMD: int MaxOuterStep: int Thermostat: int ThermostatImplemented: int * ThermostatNames: char ** TempFrequency: double alpha: double HooverMass: double TargetTemp: double ScaleTempStep: int mainname: char * defaultpath: char * pseudopotpath: char * DoOutVis: int DoOutMes: int DoOutNICS: int DoOutOrbitals: int DoOutCurrent: int DoFullCurrent: int DoPerturbation: int DoWannier: int CommonWannier: int SawtoothStart: double VectorPlane: int VectorCut: double UseAddGramSch: int Seed: int OutVisStep: int OutSrcStep: int MaxPsiStep: int EpsWannier: double MaxMinStep: int RelEpsTotalEnergy: double RelEpsKineticEnergy: double MaxMinGapStopStep: int MaxInitMinStep: int InitRelEpsTotalEnergy: double InitRelEpsKineticEnergy: double InitMaxMinGapStopStep: int ECut: double MaxLevel: int RiemannTensor: int LevRFactor: int RiemannLevel: int Lev0Factor: int RTActualUse: int AddPsis: int RCut: double StructOpt: int IsAngstroem: int RelativeCoord: int MaxTypes: int -- #config(); #~config(); #TestSyntax(const char * const filename, const periodentafel * const periode) const: int #Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList); #LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList); #RetrieveConfigPathAndName(const string filename); #Save(const char * const filename, const periodentafel * const periode, molecule * const mol) const: bool #SaveMPQC(const char * const filename, const molecule * const mol) const: bool #SavePDB(const char * const filename, const MoleculeListClass * const MolList) const: bool #SavePDB(const char * const filename, const molecule * const mol) const: bool #SaveTREMOLO(const char * const filename, const molecule * const mol) const: bool #SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const: bool #Edit(); #GetIsAngstroem() const: bool #GetDefaultPath() const: char * #SetDefaultPath(const char * const path); #InitThermostats(); #ParseThermostats(class ConfigFileBuffer * const fb);com.umlet.element.base.Relation490142863634lt=<<<<-21;21;623;21com.umlet.element.base.Relation159684121139lt=<<<<- 270;126;105;126;105;35;21;35;21;63com.umlet.element.base.Class2520980224140<<Singleton>> errorLogger -- static ostream *nix; static int verbosity; static errorLogger* instance; -- #static getInstance(): errorLogger* #static purgeInstance() #static DoOutput(): bool #static setVerbosity(int verbosityLevel); #protected errorLogger() #protected ~errorLogger()com.umlet.element.base.Class2093106436435KeyCompare -- -- #operator() (const KeySet SubgraphA, const KeySet SubgraphB) const: bool com.umlet.element.base.Class11691218147105UniqueFragments -- ANOVAOrder: int FragmentCounter: int CurrentIndex: int TEFactor: double ShortestPathList: int * UsedList: bool ** BondsPerSPCount: int *com.umlet.element.base.Relation490125369234lt=<<<<-679;21;21;21com.umlet.element.base.Relation1120980251307lt=<<<<-49;294;21;294;21;224;238;224;238;21com.umlet.element.base.Class840112724528Graph {map <KeySet, NumberValuePair, KeyCompare>} com.umlet.element.base.Relation8611134321153lt=<<<<-308;140;21;140;21;21com.umlet.element.base.Class94511905628KeySet {set<int>}com.umlet.element.base.Relation945119723790lt=<<<<-224;77;21;77;21;21com.umlet.element.base.Relation1085105799230lt=<<<<- 0...N X 0...N84;217;56;217;56;112;21;112;21;21com.umlet.element.base.Class1736228214742LSQ_params -- vectors: const Vector ** num: int com.umlet.element.base.Class104326614735lsq_params -- x: gsl_vector *com.umlet.element.base.Relation116926611834lt=<<<<-21;21;105;21