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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, int pagealignsz=1)

constructor: # atoms, alignment req. 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...

int page_align_sz

page alignment size for unbuffered kernel I/O. More...

float * pos

atom coords. unit:Angstroms. More...

float * pos_ptr

non-block-aligned pointer to pos buffer. More...

float * vel

atom velocites. unit:. More...

float * force

atom forces. unit:kcal/mol/A. 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...

QMTimestep * qm_timestep

QM timestep data (orbitals, wavefctns, etc). More...

float energy [TSENERGIES]

energies for this step. unit:kcal/mol. More...

int timesteps

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

double physical_time

physical time for this step. unit:femtoseconds. 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,

int pagealignsz = 1

)

constructor: # atoms, alignment req.

Definition at line 53 of file Timestep.C.
References a_length, alloc_aligned_ptr, alpha, b_length, beta, c_length, energy, force, gamma, n, NULL, num, page_align_sz, physical_time, pos, pos_ptr, qm_timestep, timesteps, TSENERGIES, user, user2, user3, user4, and vel.

Timestep::Timestep ( const Timestep & ts )

copy constructor.

Definition at line 80 of file Timestep.C.
References a_length, alloc_aligned_ptr, alpha, b_length, beta, c_length, energy, force, gamma, NULL, num, page_align_sz, physical_time, pos, pos_ptr, qm_timestep, timesteps, user, user2, user3, user4, and vel.

Timestep::~Timestep ( void )

destructor.

Definition at line 157 of file Timestep.C.
References force, pos_ptr, qm_timestep, 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 229 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 183 of file Timestep.C.
References alpha, b_length, beta, c_length, DEGTORAD, gamma, and vec_zero.
Referenced by get_transform_from_cell, get_transforms, and colvarproxy_vmd::update_input.

void Timestep::get_transforms ( Matrix4 & a,

Matrix4 & b,

Matrix4 & c

) const

Compute transformations from current unit cell dimensions.

Definition at line 220 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 172 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 61 of file Timestep.h.
Referenced by IMDMgr::check_event, check_timesteps, VolMapCreateCoulombPotentialMSM::compute_frame, fpbc_exec_join, fpbc_exec_join_cpu, fpbc_exec_recenter, fpbc_exec_unwrap, fpbc_exec_unwrap_cpu, fpbc_exec_wrapatomic, fpbc_exec_wrapatomic_cpu, fpbc_exec_wrapcompound, fpbc_exec_wrapcompound_cpu, measure_gofr, measure_rdf, measure_surface, VMDApp::molecule_from_selection_list, MolFilePlugin::next, py_get_periodic, py_set_periodic, Timestep, colvarproxy_vmd::update_input, and MolFilePlugin::write_timestep.

float Timestep::alpha

Size and shape of unit cell.

Definition at line 61 of file Timestep.h.
Referenced by IMDMgr::check_event, check_timesteps, VolMapCreateCoulombPotentialMSM::compute_frame, get_transform_vectors, measure_gofr, measure_rdf, measure_surface, VMDApp::molecule_from_selection_list, MolFilePlugin::next, py_get_periodic, py_set_periodic, Timestep, colvarproxy_vmd::update_input, and MolFilePlugin::write_timestep.

float Timestep::b_length

Size and shape of unit cell.

Definition at line 61 of file Timestep.h.
Referenced by IMDMgr::check_event, check_timesteps, VolMapCreateCoulombPotentialMSM::compute_frame, fpbc_exec_join, fpbc_exec_join_cpu, fpbc_exec_recenter, fpbc_exec_unwrap, fpbc_exec_unwrap_cpu, fpbc_exec_wrapatomic, fpbc_exec_wrapatomic_cpu, fpbc_exec_wrapcompound, fpbc_exec_wrapcompound_cpu, get_transform_vectors, measure_gofr, measure_rdf, measure_surface, VMDApp::molecule_from_selection_list, MolFilePlugin::next, py_get_periodic, py_set_periodic, Timestep, colvarproxy_vmd::update_input, and MolFilePlugin::write_timestep.

float Timestep::beta

Size and shape of unit cell.

Definition at line 61 of file Timestep.h.
Referenced by IMDMgr::check_event, check_timesteps, VolMapCreateCoulombPotentialMSM::compute_frame, get_transform_vectors, measure_gofr, measure_rdf, measure_surface, VMDApp::molecule_from_selection_list, MolFilePlugin::next, py_get_periodic, py_set_periodic, Timestep, colvarproxy_vmd::update_input, and MolFilePlugin::write_timestep.

float Timestep::c_length

Size and shape of unit cell.

Definition at line 61 of file Timestep.h.
Referenced by IMDMgr::check_event, check_timesteps, VolMapCreateCoulombPotentialMSM::compute_frame, fpbc_exec_join, fpbc_exec_join_cpu, fpbc_exec_recenter, fpbc_exec_unwrap, fpbc_exec_unwrap_cpu, fpbc_exec_wrapatomic, fpbc_exec_wrapatomic_cpu, fpbc_exec_wrapcompound, fpbc_exec_wrapcompound_cpu, get_transform_vectors, measure_gofr, measure_rdf, measure_surface, VMDApp::molecule_from_selection_list, MolFilePlugin::next, py_get_periodic, py_set_periodic, Timestep, colvarproxy_vmd::update_input, and MolFilePlugin::write_timestep.

float Timestep::energy[TSENERGIES]

energies for this step. unit:kcal/mol.

Definition at line 56 of file Timestep.h.
Referenced by IMDMgr::check_event, Timestep, and zero_values.

float* Timestep::force

atom forces. unit:kcal/mol/A.

Definition at line 50 of file Timestep.h.
Referenced by GeometryMol::atom_formatted_name, Molecule::get_new_frames, Timestep, and ~Timestep.

float Timestep::gamma

Size and shape of unit cell.

Definition at line 61 of file Timestep.h.
Referenced by IMDMgr::check_event, check_timesteps, VolMapCreateCoulombPotentialMSM::compute_frame, get_transform_vectors, measure_gofr, measure_rdf, measure_surface, VMDApp::molecule_from_selection_list, MolFilePlugin::next, py_get_periodic, py_set_periodic, Timestep, colvarproxy_vmd::update_input, 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, py_timestep, py_velocities, Timestep, MolFilePlugin::write_timestep, and zero_values.

int Timestep::page_align_sz

page alignment size for unbuffered kernel I/O.

Definition at line 46 of file Timestep.h.
Referenced by Timestep.

double Timestep::physical_time

physical time for this step. unit:femtoseconds.

Definition at line 58 of file Timestep.h.
Referenced by GeometryMol::atom_formatted_name, AtomColor::find, MolFilePlugin::next, py_get_physical_time, py_set_physical_time, Timestep, and MolFilePlugin::write_timestep.

float* Timestep::pos

atom coords. unit:Angstroms.

Definition at line 47 of file Timestep.h.
Referenced by GeometryMol::atom_formatted_name, atomsel_gridindex_array, atomsel_interp_volume_array, atomsel_volume_array, IMDMgr::check_event, cmd_gettimestep, cmd_rawtimestep, QMData::compute_overlap_integrals, AtomSel::coordinates, AtomColor::find, find_cluster_thr, fpbc_exec_join, fpbc_exec_join_cpu, fpbc_exec_recenter, fpbc_exec_unwrap, fpbc_exec_unwrap_cpu, fpbc_exec_wrapatomic, fpbc_exec_wrapatomic_cpu, fpbc_exec_wrapcompound, fpbc_exec_wrapcompound_cpu, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, measure_gofr, measure_pbc_neighbors, measure_rdf, VMDApp::molecule_from_selection_list, 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_timestep, PickModeMoveRep::rotate, PickModeMoveMolecule::rotate, PickModeMoveFragment::rotate, PickModeMoveResidue::rotate, Tool::target, Timestep, PickModeMoveRep::translate, PickModeMoveMolecule::translate, PickModeMoveFragment::translate, PickModeMoveResidue::translate, PickModeMoveAtom::translate, vmd_bond_search, vmd_volmap_ils, write_ss_input_pdb, MolFilePlugin::write_timestep, and zero_values.

float* Timestep::pos_ptr

non-block-aligned pointer to pos buffer.

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

QMTimestep* Timestep::qm_timestep

QM timestep data (orbitals, wavefctns, etc).

Definition at line 55 of file Timestep.h.
Referenced by molinfo_get, QMData::mullikenpop, MolFilePlugin::next, QMData::orblocalize, GraphicsFltkRepOrbital::regen_orbitallist, Timestep, and ~Timestep.

int Timestep::timesteps

timesteps elapsed so far (if known).

Definition at line 57 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 51 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 52 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 53 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 54 of file Timestep.h.
Referenced by AtomColor::find, Timestep, and ~Timestep.

float* Timestep::vel

atom velocites. unit:.

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

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

Generated on Thu Oct 30 02:47:23 2025 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, int pagealignsz=1)
	constructor: # atoms, alignment req. 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...
int	page_align_sz
	page alignment size for unbuffered kernel I/O. More...
float *	pos
	atom coords. unit:Angstroms. More...
float *	pos_ptr
	non-block-aligned pointer to pos buffer. More...
float *	vel
	atom velocites. unit:. More...
float *	force
	atom forces. unit:kcal/mol/A. 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...
QMTimestep *	qm_timestep
	QM timestep data (orbitals, wavefctns, etc). More...
float	energy [TSENERGIES]
	energies for this step. unit:kcal/mol. More...
int	timesteps
	timesteps elapsed so far (if known). More...
double	physical_time
	physical time for this step. unit:femtoseconds. 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...