QMData class Reference

Public Methods

QMData (int natoms, int nbasis, int shells, int nwave)

constructor:. More...

~QMData (void)

destructor. More...

void init_electrons (Molecule *mol, int totcharge)

Initialize total charge, multiplicity and everything that can be derived from that. More...

void delete_basis_set ()

Free memory of the basis set. More...

int init_basis (Molecule *mol, int num_basis_atoms, const char *string, const float *basis, const int *atomic_numbers, const int *nshells, const int *nprim, const int *shelltypes)

Populate basis set data and organize them into hierarcical data structures. More...

int create_unique_basis (Molecule *mol, int num_basis_atoms)

Collapse basis set so that we have one atomic basis set per atom type. More...

void normalize_basis ()

Multiply contraction coefficients with the shell dependent part of the normalization factor. More...

void init_angular_norm_factors ()

Initialize table of normalization factors containing different factors for each shell and its cartesian functions. More...

const basis_atom_t * get_basis (int atom=0) const

Get basis set for an atom. More...

const shell_t * get_basis (int atom, int shell) const

Get basis set for a shell. More...

const int * get_atom_types () const

const int * get_num_shells_per_atom () const

const int * get_num_prim_per_shell () const

int get_num_atoms ()

int get_num_types ()

int get_num_shells ()

int get_num_wavecoeff_per_atom (int atom) const

int get_wave_offset (int atom, int shell=0) const

Get the offset in the wavefunction array for given shell. More...

const char * get_shell_type_str (const shell_t *shell)

Get shell type letter (S, P, D, F, ...) followed by '0円'. More...

char * get_angular_momentum_str (int atom, int shell, int mom) const

void set_angular_momentum_str (int atom, int shell, int mom, const char *tag)

void set_angular_momentum (int atom, int shell, int mom, int *pow)

int get_angular_momentum (int atom, int shell, int mom, int comp)

int set_angular_momenta (const int *angmom)

int get_num_imag ()

int get_num_intcoords ()

void set_carthessian (int numcartcoords, double *array)

void set_inthessian (int numintcoords, double *array)

void set_normalmodes (int numcart, float *array)

void set_wavenumbers (int numcart, float *array)

void set_intensities (int numcart, float *array)

void set_imagmodes (int numimag, int *array)

const double * get_carthessian () const

const double * get_inthessian () const

const float * get_normalmodes () const

const float * get_wavenumbers () const

const float * get_intensities () const

const int * get_imagmodes () const

const char * get_scftype_string (void) const

Translate the scftype constant into a string. More...

const char * get_runtype_string (void) const

Translate the runtype constant into a string. More...

const char * get_status_string ()

Get status of SCF and optimization convergence. More...

int assign_wavef_id (int type, int spin, int excit, char *info, wavef_signa_t *(&signa_ts), int &numsig)

Determines and returns a unique ID for each wavefuntion based on it's signature (type, spin, excitation, info). More...

int find_wavef_id_from_gui_specs (int type, int spin, int exci)

Matches the wavefunction selected from the GUI buttons (type, spin, excitation) with a wavefunction IDtag. Returns -1 if no such wavefunction exists. More...

int compare_wavef_guitype_to_type (int guitype, int type)

Return 1 if the wavefunction type from the GUI matches the given type. More...

int has_wavef_guitype (int guitype)

Return 1 if we have a wavefunction with the given GUI_WAVEF_TYPE_*. More...

int has_wavef_spin (int spin)

Return 1 if we have any wavefunction with the given spin. More...

int has_wavef_exci (int exci)

Return 1 if we have any wavefunction with the given excitation. More...

int has_wavef_signa (int type, int spin, int exci)

Return 1 if we have any wavefunction with the given signature (type, spin, and excitation). More...

int get_highest_excitation (int guitype)

Get the highest excitation for any wavefunction with the given type. More...

void update_avail_orbs (int iwavesig, int norbitals, const int *orbids, const float *orbocc)

Update the list of available orbitals. More...

int get_max_avail_orbitals (int iwavesig)

Return the maximum number of available orbitals for the given wavefunction over all frames Can be used to determine the number of orbitals to be displayed in the GUI. Returns -1 if requested wavefunction doesn't exist. More...

int get_avail_orbitals (int iwavesig, int *(&orbids))

Get IDs of all orbitals available for the given wavefunction. iwavesig is the index of the wavefunction signature. Returns 1 upon success, 0 otherwise. More...

int get_avail_occupancies (int iwavesig, float *(&orbocc))

Get the occupancies of all available orbitals for the given wavefunction. More...

int get_orbital_label_from_gui_index (int iwavesig, int iorb)

For the given wavefunction signature return the iorb-th orbital label. Used to translate from the GUI list of available orbitals the unique orbital label. More...

int has_orbital (int iwavesig, int orbid)

Return 1 if the given wavefunction has an orbital with ID orbid in any frame. More...

int expand_atompos (const float *atompos, float *(&expandedpos))

int expand_basis_array (float *(&expandedbasis), int *(&numprims))

void compute_overlap_integrals (Timestep *ts, const float *expandedbasis, const int *numprims, float *(&overlap_matrix))

Compute electronic overlap integrals Sij. Memory for overlap_matrix will be allocated. More...

int mullikenpop (Timestep *ts, int iwavesig, const float *expandedbasis, const int *numprims)

double localization_orbital_change (int orbid1, int orbid2, const float *C, const float *S)

float pair_localization_measure (int num_orbitals, int orbid1, int orbid2, const float *C, const float *S)

double mean_localization_measure (int num_orbitals, const float *C, const float *S)

void rotate_2x2_orbitals (float *C, int orbid1, int orbid2, double gamma)

Perform 2x2 rotation of orbital pair. Equations (10a) and (10b) in Pipek & Mezey (1989). More...

double localization_rotation_angle (const float *C, const float *S, int orbid1, int orbid2)

Rotation angle gamma for the 2 by 2 orbital rotations Equation (9) in Boughton & Pulay (1993). More...

double gross_atom_mulliken_pop (const float *C, const float *S, int atom, int orbid) const

Return the gross Mulliken population of orbital i on atom A. More...

double orb_pair_gross_atom_mulliken_pop (const float *C, const float *S, int atom, int orbid1, int orbid2)

int orblocalize (Timestep *ts, int waveid, const float *expandedbasis, const int *numprims)

Create a new wavefunction object based on existing wavefunction "waveid" with orbitals localized using the Pipek-Mezey algorithm. More...

Orbital * create_orbital (int iwave, int orbid, float *pos, QMTimestep *qmts)

Create a new Orbital and return the pointer. User is responsible for deleting. More...

Public Attributes

int num_wave_f

max. size of the wave_function array (stored in QMTimestep). The actual number of MOs present can be different for each frame but this is the maximum number of possible occupied and virtual orbitals, i.e. this is the number of contracted cartesian gaussian basis functions or the size of the secular equation. More...

int num_basis

Number of the {exp, coeff) pairs in basis array. This is NOT the same as above since each (P, D, F, ...) shell consists of (3, 6, 10, ...) cartesian functions! More...

int num_wavef_signa

total number of wavefunctions with different signatures (over all frames). More...

int runtype

runtype for internal use. More...

int scftype

scftype for internal use. More...

int status

SCF and optimization status. More...

int nproc

number of processors used. More...

int memory

amount of memory used in MByte. More...

int num_electrons

number of electrons. More...

int totalcharge

total charge of system. More...

char * basis_string

basis name as "nice" string. More...

char runtitle [QMDATA_BIGBUFSIZ]

title of run. (large for Gaussian). More...

char geometry [QMDATA_BUFSIZ]

type of provided geometry, e.g. UNIQUE, ZMT, CART, ... More...

char version_string [QMDATA_BUFSIZ]

QM code version information. More...

QMData::QMData ( int natoms,

int nbasis,

int shells,

int nwave

)

constructor:.

Definition at line 49 of file QMData.C.

References NULL, num_wavef_signa, QMSTATUS_UNKNOWN, runtype, RUNTYPE_UNKNOWN, scftype, SCFTYPE_UNKNOWN, and status.

QMData::~QMData ( void )

destructor.

Definition at line 79 of file QMData.C.

References basis_string, delete_basis_set, and num_wavef_signa.

int QMData::assign_wavef_id ( int type,

int spin,

int excit,

char * info,

wavef_signa_t *& signa_ts,

int & numsig

)

Determines and returns a unique ID for each wavefuntion based on it's signature (type, spin, excitation, info).

Definition at line 864 of file QMData.C.

References wavef_signa_t::exci, wavef_signa_t::info, NULL, num_wavef_signa, QMDATA_BUFSIZ, wavef_signa_t::spin, and wavef_signa_t::type.

Referenced by QMTimestep::add_wavefunction.

int QMData::compare_wavef_guitype_to_type ( int guitype,

int type

)

Return 1 if the wavefunction type from the GUI matches the given type.

Definition at line 974 of file QMData.C.

References GUI_WAVEF_TYPE_CANON, GUI_WAVEF_TYPE_CINAT, GUI_WAVEF_TYPE_GEMINAL, GUI_WAVEF_TYPE_LOCAL, GUI_WAVEF_TYPE_MCSCFNAT, GUI_WAVEF_TYPE_MCSCFOPT, GUI_WAVEF_TYPE_OTHER, WAVE_BOYS, WAVE_CANON, WAVE_CINATUR, WAVE_GEMINAL, WAVE_MCSCFNAT, WAVE_MCSCFOPT, WAVE_PIPEK, WAVE_RUEDEN, and WAVE_UNKNOWN.

Referenced by find_wavef_id_from_gui_specs, get_highest_excitation, and has_wavef_guitype.

void QMData::compute_overlap_integrals ( Timestep * ts,

const float * expandedbasis,

const int * numprims,

float *& overlap_matrix

)

Compute electronic overlap integrals Sij. Memory for overlap_matrix will be allocated.

Definition at line 1463 of file QMData.C.

References expand_atompos, get_overlap_matrix, NULL, num_wave_f, and Timestep::pos.

Referenced by molinfo_get, mullikenpop, and orblocalize.

Orbital * QMData::create_orbital ( int iwave,

int orbid,

float * pos,

QMTimestep * qmts

)

Create a new Orbital and return the pointer. User is responsible for deleting.

Definition at line 1911 of file QMData.C.

References QMTimestep::get_wavecoeffs, num_basis, and num_wave_f.

int QMData::create_unique_basis ( Molecule * mol,

int num_basis_atoms

)

Collapse basis set so that we have one atomic basis set per atom type.

Definition at line 384 of file QMData.C.

References BaseMolecule::atom, basis_atom_t::atomicnum, MolAtom::atomicnumber, shell_t::basis, prim_t::coeff, compare_atomic_basis, copy_atomic_basis, delete_basis_set, prim_t::expon, get_shell_type_str, num_basis, shell_t::num_cart_func, shell_t::numprims, basis_atom_t::numshells, shell_t::prim, basis_atom_t::shell, and shell_t::type.

Referenced by init_basis.

void QMData::delete_basis_set ( )

Free memory of the basis set.

Definition at line 112 of file QMData.C.

References NULL, basis_atom_t::numshells, shell_t::prim, and basis_atom_t::shell.

Referenced by create_unique_basis, and ~QMData.

int QMData::expand_atompos ( const float * atompos,

float *& expandedpos

)

Definition at line 1148 of file QMData.C.

References n, num_wave_f, basis_atom_t::numshells, basis_atom_t::shell, shell_t::type, and z.

Referenced by compute_overlap_integrals.

int QMData::expand_basis_array ( float *& expandedbasis,

int *& numprims

)

Definition at line 1183 of file QMData.C.

References shell_t::basis, prim_t::expon, n, shell_t::norm_fac, shell_t::num_cart_func, num_wave_f, shell_t::numprims, basis_atom_t::numshells, shell_t::prim, basis_atom_t::shell, and shell_t::type.

Referenced by VMDApp::molecule_orblocalize, and molinfo_get.

int QMData::find_wavef_id_from_gui_specs ( int type,

int spin,

int exci

)

Matches the wavefunction selected from the GUI buttons (type, spin, excitation) with a wavefunction IDtag. Returns -1 if no such wavefunction exists.

Definition at line 947 of file QMData.C.

References compare_wavef_guitype_to_type, wavef_signa_t::exci, num_wavef_signa, and wavef_signa_t::spin.

Referenced by GraphicsFltkRepOrbital::regen_excitationlist, and GraphicsFltkRepOrbital::regen_orbitallist.

int QMData::get_angular_momentum ( int atom,

int shell,

int mom,

int comp

)

Definition at line 688 of file QMData.C.

References get_basis, and get_wave_offset.

char * QMData::get_angular_momentum_str ( int atom,

int shell,

int mom

) const

Definition at line 732 of file QMData.C.

References get_wave_offset, and NULL.

Referenced by molinfo_get.

const int* QMData::get_atom_types ( ) const [inline]

Definition at line 450 of file QMData.h.

int QMData::get_avail_occupancies ( int iwavesig,

float *& orbocc

)

Get the occupancies of all available orbitals for the given wavefunction.

Definition at line 1112 of file QMData.C.

References wavef_signa_t::max_avail_orbs, num_wavef_signa, and wavef_signa_t::orbocc.

int QMData::get_avail_orbitals ( int iwavesig,

int *& orbids

)

Get IDs of all orbitals available for the given wavefunction. iwavesig is the index of the wavefunction signature. Returns 1 upon success, 0 otherwise.

Definition at line 1098 of file QMData.C.

References wavef_signa_t::max_avail_orbs, num_wavef_signa, and wavef_signa_t::orbids.

const shell_t * QMData::get_basis ( int atom,

int shell

) const

Get basis set for a shell.

Definition at line 611 of file QMData.C.

References NULL.

const basis_atom_t * QMData::get_basis ( int atom = 0 ) const

Get basis set for an atom.

Definition at line 603 of file QMData.C.

References NULL.

Referenced by get_angular_momentum, molinfo_get, and Wavefunction::sort_wave_coefficients.

const double* QMData::get_carthessian ( ) const [inline]

Definition at line 484 of file QMData.h.

int QMData::get_highest_excitation ( int guitype )

Get the highest excitation for any wavefunction with the given type.

Definition at line 1024 of file QMData.C.

References compare_wavef_guitype_to_type, wavef_signa_t::exci, and num_wavef_signa.

Referenced by GraphicsFltkRepOrbital::regen_excitationlist.

const int* QMData::get_imagmodes ( ) const [inline]

Definition at line 489 of file QMData.h.

const float* QMData::get_intensities ( ) const [inline]

Definition at line 488 of file QMData.h.

const double* QMData::get_inthessian ( ) const [inline]

Definition at line 485 of file QMData.h.

int QMData::get_max_avail_orbitals ( int iwavesig )

Return the maximum number of available orbitals for the given wavefunction over all frames Can be used to determine the number of orbitals to be displayed in the GUI. Returns -1 if requested wavefunction doesn't exist.

Definition at line 1089 of file QMData.C.

References wavef_signa_t::max_avail_orbs, and num_wavef_signa.

Referenced by molinfo_get, and GraphicsFltkRepOrbital::regen_orbitallist.

const float* QMData::get_normalmodes ( ) const [inline]

Definition at line 486 of file QMData.h.

int QMData::get_num_atoms ( ) [inline]

Definition at line 454 of file QMData.h.

Referenced by Wavefunction::sort_wave_coefficients.

int QMData::get_num_imag ( ) [inline]

Definition at line 476 of file QMData.h.

Referenced by molinfo_get.

int QMData::get_num_intcoords ( ) [inline]

Definition at line 477 of file QMData.h.

Referenced by molinfo_get.

const int* QMData::get_num_prim_per_shell ( ) const [inline]

Definition at line 452 of file QMData.h.

int QMData::get_num_shells ( ) [inline]

Definition at line 456 of file QMData.h.

Referenced by molinfo_get.

const int* QMData::get_num_shells_per_atom ( ) const [inline]

Definition at line 451 of file QMData.h.

Referenced by Wavefunction::sort_wave_coefficients.

int QMData::get_num_types ( ) [inline]

Definition at line 455 of file QMData.h.

int QMData::get_num_wavecoeff_per_atom ( int atom ) const

Definition at line 619 of file QMData.C.

References shell_t::num_cart_func, basis_atom_t::numshells, and basis_atom_t::shell.

Referenced by Wavefunction::density_matrix, gross_atom_mulliken_pop, mullikenpop, orb_pair_gross_atom_mulliken_pop, and Wavefunction::population_matrix.

int QMData::get_orbital_label_from_gui_index ( int iwavesig,

int iorb

)

For the given wavefunction signature return the iorb-th orbital label. Used to translate from the GUI list of available orbitals the unique orbital label.

Definition at line 1128 of file QMData.C.

References wavef_signa_t::max_avail_orbs, num_wavef_signa, and wavef_signa_t::orbids.

const char * QMData::get_runtype_string ( void ) const

Translate the runtype constant into a string.

Definition at line 800 of file QMData.C.

References RUNTYPE_DYNAMICS, RUNTYPE_ENERGY, RUNTYPE_GRADIENT, RUNTYPE_HESSIAN, RUNTYPE_MEX, RUNTYPE_OPTIMIZE, RUNTYPE_PROPERTIES, RUNTYPE_SADPOINT, and RUNTYPE_SURFACE.

const char * QMData::get_scftype_string ( void ) const

Translate the scftype constant into a string.

Definition at line 818 of file QMData.C.

References SCFTYPE_FF, SCFTYPE_GVB, SCFTYPE_MCSCF, SCFTYPE_NONE, SCFTYPE_RHF, SCFTYPE_ROHF, and SCFTYPE_UHF.

const char * QMData::get_shell_type_str ( const shell_t * shell )

Get shell type letter (S, P, D, F, ...) followed by '0円'.

Definition at line 655 of file QMData.C.

References shell_t::type.

Referenced by create_unique_basis, and molinfo_get.

const char * QMData::get_status_string ( )

Get status of SCF and optimization convergence.

Definition at line 834 of file QMData.C.

References QMSTATUS_FILE_TRUNCATED, QMSTATUS_OPT_CONV, QMSTATUS_OPT_NOT_CONV, QMSTATUS_SCF_NOT_CONV, and status.

int QMData::get_wave_offset ( int atom,

int shell = 0

) const

Get the offset in the wavefunction array for given shell.

Definition at line 635 of file QMData.C.

Referenced by Wavefunction::density_matrix, get_angular_momentum, get_angular_momentum_str, gross_atom_mulliken_pop, molinfo_get, orb_pair_gross_atom_mulliken_pop, Wavefunction::population_matrix, set_angular_momentum, and set_angular_momentum_str.

const float* QMData::get_wavenumbers ( ) const [inline]

Definition at line 487 of file QMData.h.

double QMData::gross_atom_mulliken_pop ( const float * C,

const float * S,

int atom,

int orbid

) const

Return the gross Mulliken population of orbital i on atom A.

Definition at line 1846 of file QMData.C.

References get_num_wavecoeff_per_atom, get_wave_offset, and num_wave_f.

Referenced by localization_orbital_change, localization_rotation_angle, mean_localization_measure, and pair_localization_measure.

int QMData::has_orbital ( int iwavesig,

int orbid

)

Return 1 if the given wavefunction has an orbital with ID orbid in any frame.

Definition at line 1137 of file QMData.C.

References wavef_signa_t::max_avail_orbs, num_wavef_signa, and wavef_signa_t::orbids.

Referenced by GraphicsFltkRepOrbital::regen_orbitallist.

int QMData::has_wavef_exci ( int exci )

Return 1 if we have any wavefunction with the given excitation.

Definition at line 1000 of file QMData.C.

References wavef_signa_t::exci, and num_wavef_signa.

int QMData::has_wavef_guitype ( int guitype )

Return 1 if we have a wavefunction with the given GUI_WAVEF_TYPE_*.

Definition at line 964 of file QMData.C.

References compare_wavef_guitype_to_type, and num_wavef_signa.

Referenced by GraphicsFltkRepOrbital::regen_excitationlist, and GraphicsFltkRepOrbital::regen_wavefunctypes.

int QMData::has_wavef_signa ( int type,

int spin,

int exci

)

Return 1 if we have any wavefunction with the given signature (type, spin, and excitation).

Definition at line 1011 of file QMData.C.

References wavef_signa_t::exci, num_wavef_signa, wavef_signa_t::spin, and wavef_signa_t::type.

int QMData::has_wavef_spin ( int spin )

Return 1 if we have any wavefunction with the given spin.

Definition at line 990 of file QMData.C.

References num_wavef_signa, and wavef_signa_t::spin.

Referenced by GraphicsFltkRepOrbital::regen_wavefunctypes.

void QMData::init_angular_norm_factors ( )

Initialize table of normalization factors containing different factors for each shell and its cartesian functions.

Definition at line 570 of file QMData.C.

References fac.

Referenced by init_basis.

int QMData::init_basis ( Molecule * mol,

int num_basis_atoms,

const char * string,

const float * basis,

const int * atomic_numbers,

const int * nshells,

const int * nprim,

const int * shelltypes

)

Populate basis set data and organize them into hierarcical data structures.

Definition at line 171 of file QMData.C.

References basis_atom_t::atomicnum, shell_t::basis, basis_string, prim_t::coeff, shell_t::combo, create_unique_basis, prim_t::expon, init_angular_norm_factors, shell_t::norm_fac, normalize_basis, num_basis, shell_t::num_cart_func, shell_t::numprims, basis_atom_t::numshells, shell_t::prim, basis_atom_t::shell, SP_P_SHELL, SP_S_SHELL, SPD_D_SHELL, SPD_P_SHELL, SPD_S_SHELL, and shell_t::type.

Referenced by MolFilePlugin::read_qm_data.

void QMData::init_electrons ( Molecule * mol,

int totcharge

)

Initialize total charge, multiplicity and everything that can be derived from that.

Definition at line 130 of file QMData.C.

References BaseMolecule::atom, MolAtom::atomicnumber, num_electrons, scftype, SCFTYPE_RHF, SCFTYPE_ROHF, SCFTYPE_UHF, and totalcharge.

Referenced by MolFilePlugin::read_qm_data.

double QMData::localization_orbital_change ( int orbid1,

int orbid2,

const float * C,

const float * S

)

Definition at line 1713 of file QMData.C.

References gross_atom_mulliken_pop, and orb_pair_gross_atom_mulliken_pop.

Referenced by orblocalize.

double QMData::localization_rotation_angle ( const float * C,

const float * S,

int orbid1,

int orbid2

)

Rotation angle gamma for the 2 by 2 orbital rotations Equation (9) in Boughton & Pulay (1993).

Definition at line 1803 of file QMData.C.

References gross_atom_mulliken_pop, orb_pair_gross_atom_mulliken_pop, and VMD_PI.

Referenced by orblocalize.

double QMData::mean_localization_measure ( int num_orbitals,

const float * C,

const float * S

)

Definition at line 1756 of file QMData.C.

References gross_atom_mulliken_pop.

Referenced by orblocalize.

int QMData::mullikenpop ( Timestep * ts,

int iwavesig,

const float * expandedbasis,

const int * numprims

)

Definition at line 1500 of file QMData.C.

References compute_overlap_integrals, Wavefunction::density_matrix, Wavefunction::get_num_coeffs, get_num_wavecoeff_per_atom, QMTimestep::get_wavef_index, QMTimestep::get_wavefunction, mm_mul, num_wavef_signa, Wavefunction::population_matrix, and Timestep::qm_timestep.

void QMData::normalize_basis ( )

Multiply contraction coefficients with the shell dependent part of the normalization factor.

Definition at line 533 of file QMData.C.

References shell_t::basis, prim_t::coeff, prim_t::expon, shell_t::numprims, basis_atom_t::numshells, shell_t::prim, basis_atom_t::shell, shell_t::type, and VMD_PI.

Referenced by init_basis.

double QMData::orb_pair_gross_atom_mulliken_pop ( const float * C,

const float * S,

int atom,

int orbid1,

int orbid2

)

Definition at line 1870 of file QMData.C.

References get_num_wavecoeff_per_atom, get_wave_offset, and num_wave_f.

Referenced by localization_orbital_change, and localization_rotation_angle.

int QMData::orblocalize ( Timestep * ts,

int waveid,

const float * expandedbasis,

const int * numprims

)

Create a new wavefunction object based on existing wavefunction "waveid" with orbitals localized using the Pipek-Mezey algorithm.

Definition at line 1601 of file QMData.C.

References QMTimestep::add_wavefunction, compute_overlap_integrals, Wavefunction::get_coeffs, Wavefunction::get_excitation, Wavefunction::get_multiplicity, Wavefunction::get_num_occupied_double, Wavefunction::get_spin, QMTimestep::get_wavef_index, QMTimestep::get_wavefunction, localization_orbital_change, localization_rotation_angle, mean_localization_measure, NULL, num_wave_f, num_wavef_signa, pair_localization_measure, Timestep::qm_timestep, rotate_2x2_orbitals, and WAVE_PIPEK.

Referenced by VMDApp::molecule_orblocalize.

float QMData::pair_localization_measure ( int num_orbitals,

int orbid1,

int orbid2,

const float * C,

const float * S

)

Definition at line 1732 of file QMData.C.

References gross_atom_mulliken_pop.

Referenced by orblocalize.

void QMData::rotate_2x2_orbitals ( float * C,

int orbid1,

int orbid2,

double gamma

)

Perform 2x2 rotation of orbital pair. Equations (10a) and (10b) in Pipek & Mezey (1989).

Definition at line 1782 of file QMData.C.

References num_wave_f.

Referenced by orblocalize.

int QMData::set_angular_momenta ( const int * angmom )

Definition at line 664 of file QMData.C.

References num_wave_f.

Referenced by MolFilePlugin::read_qm_data.

void QMData::set_angular_momentum ( int atom,

int shell,

int mom,

int * pow

)

Definition at line 671 of file QMData.C.

References get_wave_offset.

void QMData::set_angular_momentum_str ( int atom,

int shell,

int mom,

const char * tag

)

Definition at line 699 of file QMData.C.

References get_wave_offset.

void QMData::set_carthessian ( int numcartcoords,

double * array

)

Definition at line 754 of file QMData.C.

Referenced by MolFilePlugin::read_qm_data.

void QMData::set_imagmodes ( int numimag,

int * array

)

Definition at line 785 of file QMData.C.

Referenced by MolFilePlugin::read_qm_data.

void QMData::set_intensities ( int numcart,

float * array

)

Definition at line 779 of file QMData.C.

Referenced by MolFilePlugin::read_qm_data.

void QMData::set_inthessian ( int numintcoords,

double * array

)

Definition at line 760 of file QMData.C.

Referenced by MolFilePlugin::read_qm_data.

void QMData::set_normalmodes ( int numcart,

float * array

)

Definition at line 767 of file QMData.C.

Referenced by MolFilePlugin::read_qm_data.

void QMData::set_wavenumbers ( int numcart,

float * array

)

Definition at line 773 of file QMData.C.

Referenced by MolFilePlugin::read_qm_data.

void QMData::update_avail_orbs ( int iwavesig,

int norbitals,

const int * orbids,

const float * orbocc

)

Update the list of available orbitals.

Definition at line 1046 of file QMData.C.

References wavef_signa_t::max_avail_orbs, wavef_signa_t::orbids, and wavef_signa_t::orbocc.

Referenced by QMTimestep::add_wavefunction.

char* QMData::basis_string

basis name as "nice" string.

Definition at line 395 of file QMData.h.

Referenced by init_basis, and ~QMData.

char QMData::geometry[QMDATA_BUFSIZ]

type of provided geometry, e.g. UNIQUE, ZMT, CART, ...

Definition at line 397 of file QMData.h.

Referenced by MolFilePlugin::read_qm_data.

int QMData::memory

amount of memory used in MByte.

Definition at line 389 of file QMData.h.

Referenced by MolFilePlugin::read_qm_data.

int QMData::nproc

number of processors used.

Definition at line 388 of file QMData.h.

Referenced by MolFilePlugin::read_qm_data.

int QMData::num_basis

Number of the {exp, coeff) pairs in basis array. This is NOT the same as above since each (P, D, F, ...) shell consists of (3, 6, 10, ...) cartesian functions!

Definition at line 292 of file QMData.h.

Referenced by create_orbital, create_unique_basis, init_basis, and Wavefunction::sort_wave_coefficients.

int QMData::num_electrons

number of electrons.

Definition at line 390 of file QMData.h.

Referenced by QMTimestep::add_wavefunction, and init_electrons.

int QMData::num_wave_f

max. size of the wave_function array (stored in QMTimestep). The actual number of MOs present can be different for each frame but this is the maximum number of possible occupied and virtual orbitals, i.e. this is the number of contracted cartesian gaussian basis functions or the size of the secular equation.

Definition at line 284 of file QMData.h.

Referenced by compute_overlap_integrals, create_orbital, expand_atompos, expand_basis_array, gross_atom_mulliken_pop, molinfo_get, orb_pair_gross_atom_mulliken_pop, orblocalize, rotate_2x2_orbitals, set_angular_momenta, and Wavefunction::sort_wave_coefficients.