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molfile_timestep_t Struct Reference

#include <molfile_plugin.h>

List of all members.

Public Attributes
float *	coords
float *	velocities
double	physical_time
float	A
float	B
float	C
float	alpha
float	beta
float	gamma

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Detailed Description

Per-timestep atom coordinates, velocities, time, energies and periodic cell info

Definition at line 238 of file molfile_plugin.h.

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Member Data Documentation

float molfile_timestep_t::A

Unit cell specification of the form A, B, C, alpha, beta, gamma. notes: A, B, C are side lengths of the unit cell alpha = angle between b and c beta = angle between a and c gamma = angle between a and b Definition at line 251 of file molfile_plugin.h. Referenced by convert_vmd_box_for_writing, convert_vmd_box_shape_to_tng, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, read_amber_cdf_timestep, read_car_timestep, read_crd_timestep, read_cube_timestep, read_dlpoly_config_timestep, read_dlpoly_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_next_timestep, read_pqr_timestep, read_rst_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_xsf_timestep, vasp_timestep_unitcell, vtf_read_next_timestep, write_crd_timestep, write_cryst1, write_hoomd_timestep, write_js_timestep, write_lammps_timestep, write_pqr_cryst1, write_rst_timestep, write_timestep, write_trr_timestep, write_vaspposcar_timestep, and xml_new_tag.

float molfile_timestep_t::alpha

Unit cell specification of the form A, B, C, alpha, beta, gamma. notes: A, B, C are side lengths of the unit cell alpha = angle between b and c beta = angle between a and c gamma = angle between a and b Definition at line 251 of file molfile_plugin.h. Referenced by convert_vmd_box_for_writing, convert_vmd_box_shape_to_tng, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, read_amber_cdf_timestep, read_car_timestep, read_crd_timestep, read_cube_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_next_timestep, read_pqr_timestep, read_rst_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_xsf_timestep, vasp_timestep_unitcell, vtf_read_next_timestep, write_cryst1, write_js_timestep, write_lammps_timestep, write_pqr_cryst1, write_rst_timestep, write_timestep, write_trr_timestep, write_vaspposcar_timestep, and xml_new_tag.

float molfile_timestep_t::B

Unit cell specification of the form A, B, C, alpha, beta, gamma. notes: A, B, C are side lengths of the unit cell alpha = angle between b and c beta = angle between a and c gamma = angle between a and b Definition at line 251 of file molfile_plugin.h. Referenced by convert_vmd_box_for_writing, convert_vmd_box_shape_to_tng, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, read_amber_cdf_timestep, read_car_timestep, read_crd_timestep, read_cube_timestep, read_dlpoly_config_timestep, read_dlpoly_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_next_timestep, read_pqr_timestep, read_rst_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_xsf_timestep, vasp_timestep_unitcell, vtf_read_next_timestep, write_crd_timestep, write_cryst1, write_hoomd_timestep, write_js_timestep, write_lammps_timestep, write_pqr_cryst1, write_rst_timestep, write_timestep, write_trr_timestep, write_vaspposcar_timestep, and xml_new_tag.

float molfile_timestep_t::beta

Unit cell specification of the form A, B, C, alpha, beta, gamma. notes: A, B, C are side lengths of the unit cell alpha = angle between b and c beta = angle between a and c gamma = angle between a and b Definition at line 251 of file molfile_plugin.h. Referenced by convert_vmd_box_for_writing, convert_vmd_box_shape_to_tng, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, read_amber_cdf_timestep, read_car_timestep, read_crd_timestep, read_cube_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_next_timestep, read_pqr_timestep, read_rst_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_xsf_timestep, vasp_timestep_unitcell, vtf_read_next_timestep, write_cryst1, write_js_timestep, write_lammps_timestep, write_pqr_cryst1, write_rst_timestep, write_timestep, write_trr_timestep, write_vaspposcar_timestep, and xml_new_tag.

float molfile_timestep_t::C

Unit cell specification of the form A, B, C, alpha, beta, gamma. notes: A, B, C are side lengths of the unit cell alpha = angle between b and c beta = angle between a and c gamma = angle between a and b Definition at line 251 of file molfile_plugin.h. Referenced by convert_vmd_box_for_writing, convert_vmd_box_shape_to_tng, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, read_amber_cdf_timestep, read_car_timestep, read_crd_timestep, read_cube_timestep, read_dlpoly_config_timestep, read_dlpoly_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_next_timestep, read_pqr_timestep, read_rst_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_xsf_timestep, vasp_timestep_unitcell, vtf_read_next_timestep, write_crd_timestep, write_cryst1, write_hoomd_timestep, write_js_timestep, write_lammps_timestep, write_pqr_cryst1, write_rst_timestep, write_timestep, write_trr_timestep, write_vaspposcar_timestep, and xml_new_tag.

float* molfile_timestep_t::coords

coordinates of all atoms, arranged xyzxyzxyz Definition at line 239 of file molfile_plugin.h. Referenced by close_hoomd_read, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, main, read_amber_cdf_timestep, read_bgf_timestep, read_car_timestep, read_cor_timestep, read_cpmd_timestep, read_crd_timestep, read_cube_timestep, read_dlpoly_config_timestep, read_dlpoly_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_mol2_timestep, read_next_timestep, read_pdbx_timestep, read_pqr_timestep, read_rst_timestep, read_timestep, LMPlugin::read_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_vasp5xdatcar_timestep, read_vaspoutcar_timestep, read_vaspposcar_timestep, read_vaspxdatcar_timestep, read_vaspxml_timestep, read_xbgf_timestep, read_xsf_timestep, read_xyz_timestep, vtf_read_next_timestep, write_bgf_timestep, write_crd_timestep, write_gro_timestep, write_hoomd_timestep, write_js_timestep, write_lammps_timestep, write_mol2_timestep, write_pqr_timestep, write_rst_timestep, write_timestep, write_tng_timestep, write_trr_timestep, write_vaspposcar_timestep, write_xbgf_timestep, write_xyz_timestep, and xml_data_block.

float molfile_timestep_t::gamma

Unit cell specification of the form A, B, C, alpha, beta, gamma. notes: A, B, C are side lengths of the unit cell alpha = angle between b and c beta = angle between a and c gamma = angle between a and b Definition at line 251 of file molfile_plugin.h. Referenced by convert_vmd_box_for_writing, convert_vmd_box_shape_to_tng, DEN_POT_WFK_read_next_timestep, GEO_read_next_timestep, read_amber_cdf_timestep, read_car_timestep, read_crd_timestep, read_cube_timestep, read_g96_timestep, read_gro_timestep, read_hoomd_structure, read_hoomd_timestep, read_js_timestep, read_lammps_timestep, read_mmtk_cdf_timestep, read_next_timestep, read_pqr_timestep, read_rst_timestep, read_tinker_timestep, read_tng_timestep, read_trr_timestep, read_xsf_timestep, vasp_timestep_unitcell, vtf_read_next_timestep, write_cryst1, write_js_timestep, write_lammps_timestep, write_pqr_cryst1, write_rst_timestep, write_timestep, write_trr_timestep, write_vaspposcar_timestep, and xml_new_tag.

double molfile_timestep_t::physical_time

physical time point associated with this frame Definition at line 254 of file molfile_plugin.h. Referenced by LMPlugin::read_timestep, read_tng_timestep, vtf_read_next_timestep, write_gro_timestep, write_hoomd_timestep, write_rst_timestep, write_tng_timestep, and xml_new_tag.

float* molfile_timestep_t::velocities

NULL unless has_velocities is set Definition at line 240 of file molfile_plugin.h. Referenced by close_hoomd_read, main, read_hoomd_structure, read_hoomd_timestep, read_lammps_timestep, read_rst_timestep, read_tng_timestep, vtf_read_next_timestep, write_gro_timestep, write_hoomd_timestep, write_rst_timestep, write_tng_timestep, and xml_data_block.

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The documentation for this struct was generated from the following file:

• molfile_plugin.h

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