|
Public Member Functions |
|
| ETCoupl (HaMolSet *new_phost_mset=NULL) |
|
HaQCMod * | GetQCMod () |
| | Get Quantum Chemical module associated with this module.
|
|
virtual void | SetDebugLevel (int new_debug_level) |
|
virtual int | OnDelAtoms (AtomCollection &del_atoms) |
| | Modify module content to react to deleted atoms.
|
| bool | clear () |
|
bool | path_coupl_calc () |
| | Perform PATHWAYS calculations (best pathway or.
|
| bool | select_important (double thresh) |
|
bool | calc_intermol_path_coupl () |
| | Calculate PATHWAYS coupling between two molecules.
|
|
bool | InitiateNodes () |
| | Initiate nodes of the connectivey graph for PATHWAYS calculations.
|
|
bool | SetEdges (int inode) |
| | Create and set Edges of the node.
|
|
bool | set_dir_path_coupl (ETEdge &edge) |
| | Set Pathway coupling for an edge.
|
|
int | GetCalcType () |
|
void | SetCalcType (const int new_calc_type) |
|
bool | DuttonModelCalc () |
| | calculations of the H_DA using Dutton Model
|
|
bool | CalcGFLocOrb () |
| | Calculate Green-Function Matrix elements from MOs.
|
|
bool | CalcGFLocOrbHeff () |
| | Calculate Green-Function Matrix elements from Heff.
|
|
int | PrintOvlpElem () |
| | Print Overlap Matrix elements for selected orbitals.
|
|
int | PrintHeffElem () |
| | Print Heff Matrix elements for selected orbitals.
|
|
bool | SetDAdipoleMat () |
| | Set the matrix of interaction of the molecule with the donor/acceptor electric field.
|
|
double | GetDAfield () |
| | Get the value of the donor/acceptor electric field.
|
|
bool | SetDAfield (double field) |
| | Set the value of the donor/acceptor electric field.
|
|
bool | FindMinSplit (double &min_field, double &min_split) |
| | Find minimal energy splitting between donor and acceptor localized eigenvectors.
|
|
bool | CreateEigVecContour (int idx, double flvl, int grid_size) |
| | build an isosurface of the eigenvector
|
|
bool | PrintEigVecCoef (int idx) |
| | Print to STDOUT expansion coefficient of the eigenvector idx.
|
|
bool | ScanEigEneField (int first_eig_val, int last_eig_val, double ifield_val, double ffield_val, double step_val) |
| | Scan eigenvalues versus donor/acceptor field.
|
|
double | calc_edge_dist () |
| | flag to calculate edge-to-edge distance between donor and acceptor
|
|
double | GetTunEne () const |
| | Get current tunneling energy.
|
|
void | SetTunEne (const double new_tun_ene) |
| | Set tunneling energy.
|
|
bool | PutSubMatToDB () |
| | Save group-group submatricies of the effective hamilonian to the database.
|
|
bool | GetSubMatFromDB () |
| | Get group-group submatricies of the effective hamilonian from the database.
|
|
bool | CalcHDAfromGF () |
| | Compute donor/acceptor coupling using donor/acceptor Green-Function.
|
|
bool | SetDAOrbFromEig () |
| | Set truncated donor/acceptor vectors (don_acc_vec) from donor/acceptor eigenstates.
|
|
bool | CalcHDAPert (double &hda_coupl) |
| | Compute donor/acceptor coupling using perturbation formula.
|
| double | GetDAsplit () const |
|
bool | SetDACoef1 () |
|
bool | PrintProtectMat () const |
| | print the diagonal of the protection matrix
|
|
bool | RecalcHeff () |
| | Recompute the effective 1e Hamiltonian matrix.
|
|
bool | DiagHeff () |
| | diagonalize the effective 1e Hamiltonian matrix
|
|
int | ZeroLongInter (double cutoff) |
| | Zero interactions beyond a cutoff distance.
|
Public Attributes |
|
vector< ETNode > | nodes |
| | Set of nodes of the graph in PATHWAYS caclulations.
|
|
bool | nodes_init_flag |
| | flag to indicate that nodes of the connectivity graph should be recomputed before PATHWAYS calculations are performed
|
|
vector< PathStep > | best_path |
| | Vector of step that make best coupled path in PATHWAYS calculations.
|
|
vector< PathStep > | coupl_map |
| | the map of best path coupling to the donor
|
|
int | ham_trunc_type |
| | hamiltonian truncation type (heff_mat,ssl,DA_dipole) or just heff_mat
|
|
HaMat_double | heff_mat |
| | the effective 1e Hamiltonian of the system
|
|
HaMat_double | ssl |
| | Overlap matrix in local orbitals.
|
|
HaMat_double | cmol |
| | Eigenstates of the Effective 1e hamiltonian.
|
|
HaVec_double | enel |
| | Eigenvalues of the Effective 1e hamiltonian.
|
|
HaMat_double | don_acc_vec |
| | vectors of donor and acceptor truncated wave functions
|
|
HaMat_double | extern_field |
| | Matrix of the of the external field to be added to effective hamiltonian.
|
| HaMat_double | protect_mat |
| HaMat_double | DA_dipole |
|
double | DA_field |
| | initial value of the electrical field in the donor-acceptor direction
|
|
HaString | db_file_name |
| | The name of the database file of the effective hamiltonian submatrices in D&Q calculations.
|
|
int | ida_eig_1 |
| | Eigen vector number corresponding to the donor.
|
|
int | ida_eig_2 |
| | Eigen vector number corresponding to the acceptor.
|
|
Operator_Type | oper_type |
|
bool | donor_orb_set |
| | Flag to show if donor orbital is set.
|
|
bool | acceptor_orb_set |
| | Flag to show if acceptor orbital is set.
|
|
int | set_da_orb_from_eig |
| int | set_dab_huck_inter |
|
double | pw_nb_decay |
| | PATHWAYS non-bond exponential distance decay parameter.
|
|
double | pw_nb_min_dist |
| | PATHWAYS non-bond minimal distance.
|
|
double | pw_hb_decay |
| | PATHWAYS H-bond exponential distance decay parameter.
|
|
double | pw_hb_min_dist |
| | PATHWAYS H-bond minimal distance.
|
|
double | pw_ln_cov_decay |
| | PATHWAYS ln of covalent bond decay parameter.
|
|
double | best_path_coupl |
| | last calculated best path value
|
|
int | log_calc_result |
| | Flag to log calculation results.
|
|
double | pw_nb_decay_intermol |
| | non-bond exp decay param for intermolecular contacts, if ==0 then use pw_nb_decay
|
|
double | nb_dist_limit |
| | maximum distance at which non-bonded contact is computed
|
|
double | tun_ene |
| | tunneling energy for Green function and perturbation calculations
|
|
int | calc_type |
| | Type of PATHWAYS calculations EST_PATH = 0, COUPL_MAP = 1;.
|
|
vector< const HaLocOrb * > | src_orbitals |
|
vector< const HaLocOrb * > | tgt_orbitals |
|
int | rebuild_mol_coupl_map |
|
PtrDoubleMap | mol1_coupl_map |
|
PtrDoubleMap | mol2_coupl_map |
Static Public Attributes |
|
int | m_hbond_paths_flag = True |
Protected Attributes |
|
HaQCMod * | ptr_qc_mod |
Friends |
|
class | ETEffHamDlg |
1.3.6