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Timestep Class Reference

Timesteps store coordinates, energies, etc. for one trajectory timestep. More...

#include <Timestep.h>

List of all members.

Public Methods

void get_transform_vectors (float v1[3], float v2[3], float v3[3]) const

Get vectors corresponding to periodic image vectors. More...

void get_transforms (Matrix4 &a, Matrix4 &b, Matrix4 &c) const

Compute transformations from current unit cell dimensions. More...

void get_transform_from_cell (const int *cell, Matrix4 &trans) const

Convert (na, nb, nc) tuple to a transformation based on the current unit cell. More...

Timestep (int n)

constructor: # atoms. More...

Timestep (const Timestep &ts)

copy constructor. More...

~Timestep (void)

destructor. More...

void zero_values ()

set the coords to 0. More...

Public Attributes

int num

number of atoms this timestep is for. More...

float * pos

coords for all atoms, as (x,y,z), (x,y,z), ... More...

float * vel

velocites for all atoms as (vx,vy,vz), ... More...

float * force

forces for all atoms. More...

float * user

Demand-allocated 1-float-per-atom 'User' data. More...

float * user2

Demand-allocated 1-float-per-atom 'User' data. More...

float * user3

Demand-allocated 1-float-per-atom 'User' data. More...

float * user4

Demand-allocated 1-float-per-atom 'User' data. More...

float energy [TSENERGIES]

energy for this step; by default, all 0. More...

int timesteps

timesteps elapsed so far (if known). More...

double physical_time

Physical time corresponding to this timestep. More...

float a_length

Size and shape of unit cell. More...

float b_length

Size and shape of unit cell. More...

float c_length

Size and shape of unit cell. More...

float alpha

Size and shape of unit cell. More...

float beta

Size and shape of unit cell. More...

float gamma

Size and shape of unit cell. More...

Detailed Description

Timesteps store coordinates, energies, etc. for one trajectory timestep.

Definition at line 43 of file Timestep.h.

Constructor & Destructor Documentation

Timestep::Timestep ( int n )

constructor: # atoms.

Definition at line 32 of file Timestep.C.
References a_length, alpha, b_length, beta, c_length, energy, force, gamma, NULL, num, physical_time, pos, timesteps, TSENERGIES, user, user2, user3, user4, and vel.

Timestep::Timestep ( const Timestep & ts )

copy constructor.

Definition at line 50 of file Timestep.C.
References a_length, alpha, b_length, beta, c_length, energy, force, gamma, NULL, num, physical_time, pos, timesteps, user, user2, user3, user4, and vel.

Timestep::~Timestep ( void )

destructor.

Definition at line 111 of file Timestep.C.
References force, pos, user, user2, user3, user4, and vel.

Member Function Documentation

void Timestep::get_transform_from_cell ( const int * cell,

Matrix4 & trans

) const

Convert (na, nb, nc) tuple to a transformation based on the current unit cell.

Definition at line 176 of file Timestep.C.
References get_transform_vectors, Matrix4::identity, Matrix4::mat, and mat.
Referenced by normal_atom_coord, GeometryMol::normal_atom_coord, PickModeCenter::pick_molecule_end, and PickModeMove::pick_molecule_move.

void Timestep::get_transform_vectors ( float v1[3],

float v2[3],

float v3[3]

) const

Get vectors corresponding to periodic image vectors.

Definition at line 132 of file Timestep.C.
References alpha, b_length, beta, c_length, DEGTORAD, gamma, and vec_zero.
Referenced by get_transform_from_cell, and get_transforms.

void Timestep::get_transforms ( Matrix4 & a,

Matrix4 & b,

Matrix4 & c

) const

Compute transformations from current unit cell dimensions.

Definition at line 168 of file Timestep.C.
References get_transform_vectors, and Matrix4::translate.
Referenced by compute_pbcminmax, measure_pbc2onc, and measure_pbc_neighbors.

void Timestep::zero_values ( )

set the coords to 0.

Definition at line 122 of file Timestep.C.
References energy, num, pos, timesteps, and TSENERGIES.
Referenced by DrawMolecule::duplicate_frame.

Member Data Documentation

float Timestep::a_length

Size and shape of unit cell.

Definition at line 59 of file Timestep.h.
Referenced by get_periodic, measure_gofr, measure_surface, MolFilePlugin::next, set_periodic, Timestep, and MolFilePlugin::write_timestep.

float Timestep::alpha

Size and shape of unit cell.

Definition at line 59 of file Timestep.h.
Referenced by get_periodic, get_transform_vectors, measure_gofr, measure_surface, MolFilePlugin::next, set_periodic, Timestep, and MolFilePlugin::write_timestep.

float Timestep::b_length

Size and shape of unit cell.

Definition at line 59 of file Timestep.h.
Referenced by get_periodic, get_transform_vectors, measure_gofr, measure_surface, MolFilePlugin::next, set_periodic, Timestep, and MolFilePlugin::write_timestep.

float Timestep::beta

Size and shape of unit cell.

Definition at line 59 of file Timestep.h.
Referenced by get_periodic, get_transform_vectors, measure_gofr, measure_surface, MolFilePlugin::next, set_periodic, Timestep, and MolFilePlugin::write_timestep.

float Timestep::c_length

Size and shape of unit cell.

Definition at line 59 of file Timestep.h.
Referenced by get_periodic, get_transform_vectors, measure_gofr, measure_surface, MolFilePlugin::next, set_periodic, Timestep, and MolFilePlugin::write_timestep.

float Timestep::energy[TSENERGIES]

energy for this step; by default, all 0.

Definition at line 54 of file Timestep.h.
Referenced by IMDMgr::check_event, Timestep, and zero_values.

float* Timestep::force

forces for all atoms.

Definition at line 48 of file Timestep.h.
Referenced by Molecule::get_new_frames, Timestep, and ~Timestep.

float Timestep::gamma

Size and shape of unit cell.

Definition at line 59 of file Timestep.h.
Referenced by get_periodic, get_transform_vectors, measure_gofr, measure_surface, MolFilePlugin::next, set_periodic, Timestep, and MolFilePlugin::write_timestep.

int Timestep::num

number of atoms this timestep is for.

Definition at line 45 of file Timestep.h.
Referenced by measure_pbc_neighbors, Timestep, timestep, velocities, MolFilePlugin::write_timestep, and zero_values.

double Timestep::physical_time

Physical time corresponding to this timestep.

Definition at line 56 of file Timestep.h.
Referenced by AtomColor::find, get_physical_time, MolFilePlugin::next, set_physical_time, and Timestep.

float* Timestep::pos

coords for all atoms, as (x,y,z), (x,y,z), ...

Definition at line 46 of file Timestep.h.
Referenced by atomsel_gridindex_array, atomsel_interp_volume_array, atomsel_volume_array, IMDMgr::check_event, cmd_gettimestep, cmd_rawtimestep, AtomSel::coordinates, AtomColor::find, measure_gofr, measure_pbc_neighbors, minmax, MolFilePlugin::next, normal_atom_coord, GeometryMol::normal_atom_coord, PickModeCenter::pick_molecule_end, PickModeMove::pick_molecule_move, PickModeForceFragment::pick_molecule_move, PickModeForceResidue::pick_molecule_move, PickModeForceAtom::pick_molecule_move, print_atom_info, py_rmsd, PickModeMoveRep::rotate, PickModeMoveMolecule::rotate, PickModeMoveFragment::rotate, PickModeMoveResidue::rotate, Tool::target, Timestep, timestep, PickModeMoveRep::translate, PickModeMoveMolecule::translate, PickModeMoveFragment::translate, PickModeMoveResidue::translate, PickModeMoveAtom::translate, vmd_bond_search, write_stride_record, MolFilePlugin::write_timestep, zero_values, and ~Timestep.

int Timestep::timesteps

timesteps elapsed so far (if known).

Definition at line 55 of file Timestep.h.
Referenced by IMDMgr::check_event, molinfo_get, molinfo_set, Timestep, and zero_values.

float* Timestep::user

Demand-allocated 1-float-per-atom 'User' data.

Definition at line 49 of file Timestep.h.
Referenced by AtomColor::find, Timestep, and ~Timestep.

float* Timestep::user2

Demand-allocated 1-float-per-atom 'User' data.

Definition at line 50 of file Timestep.h.
Referenced by AtomColor::find, Timestep, and ~Timestep.

float* Timestep::user3

Demand-allocated 1-float-per-atom 'User' data.

Definition at line 51 of file Timestep.h.
Referenced by AtomColor::find, Timestep, and ~Timestep.

float* Timestep::user4

Demand-allocated 1-float-per-atom 'User' data.

Definition at line 52 of file Timestep.h.
Referenced by AtomColor::find, Timestep, and ~Timestep.

float* Timestep::vel

velocites for all atoms as (vx,vy,vz), ...

Definition at line 47 of file Timestep.h.
Referenced by AtomColor::find, MolFilePlugin::next, Timestep, velocities, MolFilePlugin::write_timestep, and ~Timestep.

The documentation for this class was generated from the following files:

Generated on Sun Jul 6 01:28:40 2008 for VMD (current) by

Public Methods
void	get_transform_vectors (float v1[3], float v2[3], float v3[3]) const
	Get vectors corresponding to periodic image vectors. More...
void	get_transforms (Matrix4 &a, Matrix4 &b, Matrix4 &c) const
	Compute transformations from current unit cell dimensions. More...
void	get_transform_from_cell (const int *cell, Matrix4 &trans) const
	Convert (na, nb, nc) tuple to a transformation based on the current unit cell. More...
	Timestep (int n)
	constructor: # atoms. More...
	Timestep (const Timestep &ts)
	copy constructor. More...
	~Timestep (void)
	destructor. More...
void	zero_values ()
	set the coords to 0. More...
Public Attributes
int	num
	number of atoms this timestep is for. More...
float *	pos
	coords for all atoms, as (x,y,z), (x,y,z), ... More...
float *	vel
	velocites for all atoms as (vx,vy,vz), ... More...
float *	force
	forces for all atoms. More...
float *	user
	Demand-allocated 1-float-per-atom 'User' data. More...
float *	user2
	Demand-allocated 1-float-per-atom 'User' data. More...
float *	user3
	Demand-allocated 1-float-per-atom 'User' data. More...
float *	user4
	Demand-allocated 1-float-per-atom 'User' data. More...
float	energy [TSENERGIES]
	energy for this step; by default, all 0. More...
int	timesteps
	timesteps elapsed so far (if known). More...
double	physical_time
	Physical time corresponding to this timestep. More...
float	a_length
	Size and shape of unit cell. More...
float	b_length
	Size and shape of unit cell. More...
float	c_length
	Size and shape of unit cell. More...
float	alpha
	Size and shape of unit cell. More...
float	beta
	Size and shape of unit cell. More...
float	gamma
	Size and shape of unit cell. More...