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MeasurePBC.C File Reference

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "Measure.h"
#include "AtomSel.h"
#include "Matrix4.h"
#include "utilities.h"
#include "SpatialSearch.h"
#include "MoleculeList.h"
#include "Inform.h"
#include "Timestep.h"
#include "VMDApp.h"

Go to the source code of this file.

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)

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Function Documentation

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.

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