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ls1-MarDyn
ls1-MarDyn molecular dynamics code
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This is the complete list of members for FullMolecule, including all inherited members.
| _component | FullMolecule | protected |
| _F | FullMolecule | protected |
| _I (defined in FullMolecule) | FullMolecule | protected |
| _id | FullMolecule | protected |
| _invI (defined in FullMolecule) | FullMolecule | protected |
| _L | FullMolecule | protected |
| _M | FullMolecule | protected |
| _m | FullMolecule | protected |
| _q | FullMolecule | protected |
| _r | FullMolecule | protected |
| _soa (defined in FullMolecule) | FullMolecule | protected |
| _soa_index_c (defined in FullMolecule) | FullMolecule | protected |
| _soa_index_d (defined in FullMolecule) | FullMolecule | protected |
| _soa_index_lj (defined in FullMolecule) | FullMolecule | protected |
| _soa_index_q (defined in FullMolecule) | FullMolecule | protected |
| _v | FullMolecule | protected |
| _Vi (defined in FullMolecule) | FullMolecule | protected |
| buildOwnSoA() override | FullMolecule | virtual |
| calcFM() override | FullMolecule | virtual |
| calcFM_site(const std::array< double, 3 > &d, const std::array< double, 3 > &F) | FullMolecule | protected |
| calculate_mv2_Iw2(double &summv2, double &sumIw2) override | FullMolecule | virtual |
| calculate_mv2_Iw2(double &summv2, double &sumIw2, double offx, double offy, double offz) override (defined in FullMolecule) | FullMolecule | virtual |
| charge_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| charge_d_abs(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| charge_F(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| check(unsigned long id) override | FullMolecule | virtual |
| clearFM() override | FullMolecule | virtual |
| component() const override | FullMolecule | inlinevirtual |
| componentid() const (defined in MoleculeInterface) | MoleculeInterface | inline |
| computeCharge_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| computeDipole_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| computeDipole_e(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| computeLJcenter_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| computeQuadrupole_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| computeQuadrupole_e(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| convert_double_to_vcp_real_calc(const std::array< double, 3 > &v) (defined in MoleculeInterface) | MoleculeInterface | inlinestatic |
| D(unsigned short d) const override | FullMolecule | inlinevirtual |
| D_arr() const (defined in MoleculeInterface) | MoleculeInterface | inline |
| dipole_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| dipole_d_abs(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| dipole_e(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| dipole_F(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| dist2(const FullMolecule &molecule2, double dr[3]) const | FullMolecule | inline |
| dist2(const MoleculeInterface &molecule2, double dr[3]) const (defined in MoleculeInterface) | MoleculeInterface | inline |
| ee_upd_postF(double dt, double &summv2) (defined in MoleculeInterface) | MoleculeInterface | inline |
| ee_upd_preF(double dt) (defined in MoleculeInterface) | MoleculeInterface | inline |
| F(unsigned short d) const override | FullMolecule | inlinevirtual |
| F2() const override | FullMolecule | inlinevirtual |
| F_arr() (defined in MoleculeInterface) | MoleculeInterface | inlinevirtual |
| Fadd(const double a[]) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| Fchargeadd(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fchargesub(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fdipoleadd(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fdipolesub(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fljcenteradd(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fljcentersub(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fquadrupoleadd(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| Fquadrupolesub(unsigned int i, double a[]) override (defined in FullMolecule) | FullMolecule | virtual |
| FullMolecule(unsigned long id=0, Component *component=nullptr, double rx=0., double ry=0., double rz=0., double vx=0., double vy=0., double vz=0., double q0=1., double q1=1., double q2=0., double q3=0., double Dx=0., double Dy=0., double Dz=0.) (defined in FullMolecule) | FullMolecule | |
| FullMolecule(const FullMolecule &m) (defined in FullMolecule) | FullMolecule | |
| getComponentLookUpID() const override | FullMolecule | inlinevirtual |
| getI(unsigned short d) const override | FullMolecule | inlinevirtual |
| getID() const override | FullMolecule | inlinevirtual |
| getWriteFormat() | FullMolecule | static |
| inBox(const double l[3], const double u[3]) const | MoleculeInterface | inlinevirtual |
| isLessThan(const MoleculeInterface &m2) const | MoleculeInterface | |
| L2() const override | FullMolecule | inlinevirtual |
| ljcenter_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| ljcenter_d_abs(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| ljcenter_F(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| M(unsigned short d) const override | FullMolecule | inlinevirtual |
| M2() const override | FullMolecule | inlinevirtual |
| M_arr() (defined in MoleculeInterface) | MoleculeInterface | inlinevirtual |
| Madd(const double a[]) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| mass() const override | FullMolecule | inlinevirtual |
| move(int d, double dr) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| normalizeQuaternion() override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| numCharges() const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| numDipoles() const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| numLJcenters() const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| numOrientedSites() const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| numQuadrupoles() const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| numSites() const override | FullMolecule | inlinevirtual |
| operator=(const FullMolecule &m) (defined in FullMolecule) | FullMolecule | |
| orientationAngle(const MoleculeInterface &molecule2, double dr[3], double d2) const (defined in MoleculeInterface) | MoleculeInterface | inline |
| q() const override | FullMolecule | inlinevirtual |
| quadrupole_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| quadrupole_d_abs(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| quadrupole_e(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| quadrupole_F(unsigned int i) const override (defined in FullMolecule) | FullMolecule | virtual |
| r(unsigned short d) const override | FullMolecule | inlinevirtual |
| r_arr() const (defined in MoleculeInterface) | MoleculeInterface | inline |
| releaseOwnSoA() override | FullMolecule | virtual |
| scale_D(double s) (defined in MoleculeInterface) | MoleculeInterface | inline |
| scale_F(double s) (defined in MoleculeInterface) | MoleculeInterface | inline |
| scale_M(double s) (defined in MoleculeInterface) | MoleculeInterface | inline |
| scale_v(double s) (defined in MoleculeInterface) | MoleculeInterface | inline |
| scale_v(double s, double offx, double offy, double offz) (defined in MoleculeInterface) | MoleculeInterface | inline |
| setComponent(Component *component) override | FullMolecule | inlinevirtual |
| setD(unsigned short d, double D) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| setF(unsigned short d, double F) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| setF(double F[3]) override | FullMolecule | inlinevirtual |
| setid(unsigned long id) override | FullMolecule | inlinevirtual |
| setM(double M[3]) override | FullMolecule | inlinevirtual |
| setq(Quaternion q) override | FullMolecule | inlinevirtual |
| setr(unsigned short d, double r) override | FullMolecule | inlinevirtual |
| setSoA(CellDataSoABase *s) override (defined in FullMolecule) | FullMolecule | virtual |
| setStartIndexSoA_C(unsigned i) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| setStartIndexSoA_D(unsigned i) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| setStartIndexSoA_LJ(unsigned i) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| setStartIndexSoA_Q(unsigned i) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| setupSoACache(CellDataSoABase *s, unsigned iLJ, unsigned iC, unsigned iD, unsigned iQ) override (defined in FullMolecule) | FullMolecule | virtual |
| setv(unsigned short d, double v) override | FullMolecule | inlinevirtual |
| setVi(double Vi[3]) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| site_d(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| site_d_abs(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| site_F(unsigned int i) const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| totalMemsize() const override | FullMolecule | virtual |
| U_kin() override | FullMolecule | inlinevirtual |
| U_rot() override | FullMolecule | virtual |
| U_rot_2() override (defined in FullMolecule) | FullMolecule | virtual |
| U_trans() const override | FullMolecule | inlinevirtual |
| U_trans_2() const override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| upd_postF(double dt_halve, double &summv2, double &sumIw2) override | FullMolecule | virtual |
| upd_preF(double dt) override | FullMolecule | virtual |
| updateMassInertia() override | FullMolecule | inlinevirtual |
| v(unsigned short d) const override | FullMolecule | inlinevirtual |
| v2() const override | FullMolecule | inlinevirtual |
| v_arr() const (defined in MoleculeInterface) | MoleculeInterface | inline |
| vadd(const double ax, const double ay, const double az) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| Vi(unsigned short d) const override | FullMolecule | inlinevirtual |
| Vi_arr() (defined in MoleculeInterface) | MoleculeInterface | inlinevirtual |
| Viadd(const double a[]) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| vsub(const double ax, const double ay, const double az) override (defined in FullMolecule) | FullMolecule | inlinevirtual |
| write(std::ostream &ostrm) const override | FullMolecule | virtual |
| writeBinary(std::ostream &ostrm) const override | FullMolecule | virtual |
| ~FullMolecule() override (defined in FullMolecule) | FullMolecule | inline |
| ~MoleculeInterface() (defined in MoleculeInterface) | MoleculeInterface | inlinevirtual |
1.9.2