MeasurePBC.C File Reference

Functions

void orthonormal_basis (const float b[9], float e[9])

void basis_change (const float *base, const float *obase, float *newcoor, int n)

int measure_pbc2onc (MoleculeList *mlist, int molid, int frame, const float origin[3], Matrix4 &transform)

void get_transform_to_orthonormal_cell (const float *cell, const float *center, Matrix4 &transform)

int measure_pbc_neighbors (MoleculeList *mlist, AtomSel *sel, int molid, int frame, const Matrix4 *alignment, const float *center, const float *cutoff, const float *box, ResizeArray< float > *extcoord_array, ResizeArray< int > *indexmap_array)

int compute_pbcminmax (MoleculeList *mlist, int molid, int frame, const float *center, const Matrix4 *transform, float *min, float *max)

void basis_change ( const float * base,

const float * obase,

float * newcoor,

int n

)

Definition at line 58 of file MeasurePBC.C.

References dot_prod, and n.

Referenced by get_transform_to_orthonormal_cell.

int compute_pbcminmax ( MoleculeList * mlist,

int molid,

int frame,

const float * center,

const Matrix4 * transform,

float * min,

float * max

)

Definition at line 652 of file MeasurePBC.C.

References dot_prod, DrawMolecule::get_frame, Timestep::get_transforms, Matrix4::mat, MEASURE_ERR_NOFRAMES, MEASURE_ERR_NOMOLECULE, MEASURE_NOERR, MoleculeList::mol_from_id, Matrix4::multpoint3d, n, vec_copy, and vec_scaled_add.

Referenced by vmd_measure_pbc_neighbors.

void get_transform_to_orthonormal_cell ( const float * cell,

const float * center,

Matrix4 & transform

)

Definition at line 134 of file MeasurePBC.C.

References basis_change, Matrix4::inverse, Matrix4::multmatrix, orthonormal_basis, trans_from_rotate, Matrix4::translate, vec_copy, vec_negate, and vec_scaled_add.

Referenced by measure_pbc2onc, and measure_pbc_neighbors.

int measure_pbc2onc ( MoleculeList * mlist,

int molid,

int frame,

const float origin[3],

Matrix4 & transform

)

Definition at line 70 of file MeasurePBC.C.

References DrawMolecule::frame, DrawMolecule::get_frame, get_transform_to_orthonormal_cell, Timestep::get_transforms, Matrix4::mat, MEASURE_ERR_NOFRAMES, MEASURE_ERR_NOMOLECULE, MEASURE_NOERR, MoleculeList::mol_from_id, and DrawMolecule::numframes.

Referenced by vmd_measure_pbc2onc_transform.

int measure_pbc_neighbors ( MoleculeList * mlist,

AtomSel * sel,

int molid,

int frame,

const Matrix4 * alignment,

const float * center,

const float * cutoff,

const float * box,

ResizeArray< float > * extcoord_array,

ResizeArray< int > * indexmap_array

)

Definition at line 228 of file MeasurePBC.C.

References ResizeArray::append, ResizeArray::append3, ResizeArray::clear, dot_prod, find_within, DrawMolecule::frame, DrawMolecule::get_frame, get_transform_to_orthonormal_cell, Timestep::get_transforms, Matrix4::identity, Matrix4::inverse, Matrix4::loadmatrix, Matrix4::mat, MEASURE_ERR_BADCUTOFF, MEASURE_ERR_NOFRAMES, MEASURE_ERR_NOMOLECULE, MEASURE_NOERR, MoleculeList::mol_from_id, Matrix4::multmatrix, Matrix4::multpoint3d, ResizeArray::num, Timestep::num, AtomSel::num_atoms, DrawMolecule::numframes, AtomSel::on, Timestep::pos, AtomSel::selected, vec_add, vec_copy, vec_negate, vec_scale, vec_scaled_add, and vec_sub.

Referenced by vmd_measure_pbc_neighbors.

void orthonormal_basis ( const float b[9],

float e[9]

)

Definition at line 39 of file MeasurePBC.C.

References dot_prod, vec_copy, vec_normalize, and vec_triad.

Referenced by get_transform_to_orthonormal_cell.

MeasurePBC.C File Reference

Functions

Function Documentation