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xsfplugin.C File Reference

#include "largefiles.h"
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "molfile_plugin.h"
#include "periodic_table.h"

Go to the source code of this file.

Compounds
struct	xsf_box
struct	xsf_t
Defines
#define	M_PI_2   1.57079632679489661922
Enumerations
enum	xsf_keyword_t {   xsf_UNKNOWN = 0, xsf_COMMENT, xsf_BEGINFO, xsf_ENDINFO,   xsf_BEG_2D_BLOCK, xsf_END_2D_BLOCK, xsf_BEG_2D_DATA, xsf_END_2D_DATA,   xsf_BEG_3D_BLOCK, xsf_END_3D_BLOCK, xsf_BEG_3D_DATA, xsf_END_3D_DATA,   xsf_BEG_3D_BAND, xsf_END_3D_BAND, xsf_ATOMS, xsf_ANIMSTEPS,   xsf_BAND, xsf_MOLECULE, xsf_POLYMER, xsf_SLAB,   xsf_CRYSTAL, xsf_PRIMVEC, xsf_CONVVEC, xsf_PRIMCOORD,   xsf_CONVCOORD, xsf_NR_KEYWORDS }
Functions
xsf_keyword_t	lookup_keyword (const char *word)
int	xsf_readbox (xsf_box *box, float *x, float *y, float *z)
void	xsf_buildrotmat (xsf_t *xsf, float *a, float *b)
void	xsf_buildinvmat (xsf_t *xsf, float *a, float *b, float *c)
void	eatline (FILE *fd)
bool	xsf_read_cell (FILE *fd, float *a, float *b, float *c)
void	close_xsf_read (void *v)
void *	open_xsf_read (const char *filepath, const char *filetype, int *natoms)
int	read_xsf_structure (void *v, int *optflags, molfile_atom_t *atoms)
int	read_xsf_timestep (void *v, int natoms, molfile_timestep_t *ts)
int	read_xsf_metadata (void *v, int *nvolsets, molfile_volumetric_t **metadata)
int	read_xsf_data (void *v, int set, float *datablock, float *colorblock)
VMDPLUGIN_API int	VMDPLUGIN_init (void)
VMDPLUGIN_API int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int	VMDPLUGIN_fini (void)
Variables
const char *	xsf_symtab []
struct {
const char *   name
xsf_keyword_t   kw
}	xsf_aliases []
molfile_plugin_t	plugin

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Define Documentation

#define M_PI_2   1.57079632679489661922

Definition at line 29 of file xsfplugin.C. Referenced by xsf_readbox.

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Enumeration Type Documentation

enum xsf_keyword_t

Enumeration values: xsf_UNKNOWN  xsf_COMMENT  xsf_BEGINFO  xsf_ENDINFO  xsf_BEG_2D_BLOCK  xsf_END_2D_BLOCK  xsf_BEG_2D_DATA  xsf_END_2D_DATA  xsf_BEG_3D_BLOCK  xsf_END_3D_BLOCK  xsf_BEG_3D_DATA  xsf_END_3D_DATA  xsf_BEG_3D_BAND  xsf_END_3D_BAND  xsf_ATOMS  xsf_ANIMSTEPS  xsf_BAND  xsf_MOLECULE  xsf_POLYMER  xsf_SLAB  xsf_CRYSTAL  xsf_PRIMVEC  xsf_CONVVEC  xsf_PRIMCOORD  xsf_CONVCOORD  xsf_NR_KEYWORDS  Definition at line 48 of file xsfplugin.C. Referenced by lookup_keyword, and open_xsf_read.

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Function Documentation

void close_xsf_read (  void *    v )  [static]

Definition at line 888 of file xsfplugin.C. References xsf_t::fd, xsf_t::file_name, and xsf_t::vol. Referenced by VMDPLUGIN_init.

void eatline (  FILE *    fd )  [static]

Definition at line 231 of file xsfplugin.C. Referenced by analyze_traj, count_orbitals, get_basis, get_basis_options, get_cart_hessian, get_contrl, get_contrl_firefly, get_esp_charges, get_gradient, get_guess_options, get_input_structure, get_int_coords, get_int_hessian, get_job_info, get_normal_modes, get_population, get_proc_mem, get_scfdata, get_traj_frame, get_wavefunction, open_edm_read, open_molden_read, open_xsf_read, read_edm_data, read_geom_block, read_molden_structure, read_wave_coeffs, read_xsf_data, read_xsf_structure, and read_xsf_timestep.

xsf_keyword_t lookup_keyword (  const char *    word )  [static]

Definition at line 79 of file xsfplugin.C. References name, xsf_aliases, xsf_keyword_t, xsf_NR_KEYWORDS, xsf_symtab, and xsf_UNKNOWN. Referenced by open_xsf_read, read_xsf_structure, and read_xsf_timestep.

void* open_xsf_read (  const char *    filepath, const char *    filetype, int *    natoms )  [static]

Definition at line 247 of file xsfplugin.C. References xsf_t::coord, molfile_volumetric_t::dataname, eatline, xsf_t::fd, xsf_t::file_name, molfile_volumetric_t::has_color, kw, lookup_keyword, xsf_t::numatoms, xsf_t::numsteps, xsf_t::numvolmeta, xsf_t::nvolsets, molfile_volumetric_t::origin, xsf_t::origin, xsf_t::pbctype, xsf_t::rotmat, xsf_t::vol, molfile_volumetric_t::xaxis, xsf_ANIMSTEPS, xsf_ATOMS, xsf_BEG_2D_BLOCK, xsf_BEG_3D_BLOCK, xsf_BEG_3D_DATA, xsf_buildrotmat, xsf_COMMENT, xsf_CONVCOORD, xsf_CONVVEC, xsf_CRYSTAL, xsf_END_2D_BLOCK, xsf_END_3D_BLOCK, xsf_END_3D_DATA, xsf_keyword_t, xsf_MOLECULE, xsf_POLYMER, xsf_PRIMCOORD, xsf_PRIMVEC, xsf_read_cell, xsf_SLAB, xsf_UNKNOWN, molfile_volumetric_t::xsize, molfile_volumetric_t::yaxis, molfile_volumetric_t::ysize, molfile_volumetric_t::zaxis, and molfile_volumetric_t::zsize. Referenced by VMDPLUGIN_init.

int read_xsf_data (  void *    v, int    set, float *    datablock, float *    colorblock )  [static]

Definition at line 842 of file xsfplugin.C. References molfile_volumetric_t::dataname, eatline, xsf_t::fd, MOLFILE_ERROR, xsf_t::vol, molfile_volumetric_t::xsize, molfile_volumetric_t::ysize, and molfile_volumetric_t::zsize. Referenced by VMDPLUGIN_init.

int read_xsf_metadata (  void *    v, int *    nvolsets, molfile_volumetric_t **    metadata )  [static]

Definition at line 833 of file xsfplugin.C. References xsf_t::nvolsets, and xsf_t::vol. Referenced by VMDPLUGIN_init.

int read_xsf_structure (  void *    v, int *    optflags, molfile_atom_t *    atoms )  [static]

Definition at line 531 of file xsfplugin.C. References xsf_box::A, xsf_box::alpha, molfile_atom_t::atomicnumber, xsf_box::B, xsf_box::beta, xsf_t::box, xsf_box::C, molfile_atom_t::chain, eatline, xsf_t::fd, xsf_t::file_name, xsf_box::gamma, get_pte_idx, get_pte_mass, get_pte_vdw_radius, xsf_t::invmat, lookup_keyword, molfile_atom_t::mass, MOLFILE_ATOMICNUMBER, MOLFILE_ERROR, MOLFILE_MASS, MOLFILE_RADIUS, molfile_atom_t::name, xsf_t::numatoms, molfile_atom_t::radius, molfile_atom_t::resid, molfile_atom_t::resname, xsf_t::rotmat, molfile_atom_t::segid, molfile_atom_t::type, xsf_ATOMS, xsf_buildinvmat, xsf_buildrotmat, xsf_PRIMCOORD, xsf_PRIMVEC, xsf_read_cell, and xsf_readbox. Referenced by VMDPLUGIN_init.

int read_xsf_timestep (  void *    v, int    natoms, molfile_timestep_t *    ts )  [static]

Definition at line 661 of file xsfplugin.C. References xsf_box::A, molfile_timestep_t::A, xsf_box::alpha, molfile_timestep_t::alpha, xsf_box::B, molfile_timestep_t::B, xsf_box::beta, molfile_timestep_t::beta, xsf_t::box, xsf_box::C, molfile_timestep_t::C, xsf_box::cell, molfile_timestep_t::coords, eatline, xsf_t::fd, xsf_t::file_name, xsf_box::gamma, molfile_timestep_t::gamma, xsf_t::invmat, lookup_keyword, MOLFILE_ERROR, xsf_t::origin, xsf_t::pbctype, xsf_t::rotmat, xsf_ATOMS, xsf_buildinvmat, xsf_buildrotmat, xsf_CRYSTAL, xsf_MOLECULE, xsf_POLYMER, xsf_PRIMCOORD, xsf_PRIMVEC, xsf_read_cell, xsf_readbox, and xsf_SLAB. Referenced by VMDPLUGIN_init.

VMDPLUGIN_API int VMDPLUGIN_fini (  void    )

Definition at line 929 of file xsfplugin.C. References VMDPLUGIN_API, and VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init (  void    )

Definition at line 904 of file xsfplugin.C. References molfile_plugin_t::close_file_read, close_xsf_read, molfile_plugin_t::filename_extension, MOLFILE_PLUGIN_TYPE, molfile_plugin_t::open_file_read, open_xsf_read, molfile_plugin_t::read_next_timestep, molfile_plugin_t::read_structure, molfile_plugin_t::read_volumetric_data, molfile_plugin_t::read_volumetric_metadata, read_xsf_data, read_xsf_metadata, read_xsf_structure, read_xsf_timestep, vmdplugin_ABIVERSION, VMDPLUGIN_API, VMDPLUGIN_SUCCESS, and VMDPLUGIN_THREADSAFE.

VMDPLUGIN_API int VMDPLUGIN_register (  void *    v, vmdplugin_register_cb    cb )

Definition at line 924 of file xsfplugin.C. References VMDPLUGIN_API, vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

void xsf_buildinvmat (  xsf_t *    xsf, float *    a, float *    b, float *    c )  [static]

Definition at line 211 of file xsfplugin.C. References xsf_t::invmat. Referenced by read_xsf_structure, and read_xsf_timestep.

void xsf_buildrotmat (  xsf_t *    xsf, float *    a, float *    b )  [static]

Definition at line 181 of file xsfplugin.C. References xsf_t::rotmat. Referenced by open_xsf_read, read_xsf_structure, and read_xsf_timestep.

bool xsf_read_cell (  FILE *    fd, float *    a, float *    b, float *    c )  [static]

Definition at line 237 of file xsfplugin.C. Referenced by open_xsf_read, read_xsf_structure, and read_xsf_timestep.

int xsf_readbox (  xsf_box *    box, float *    x, float *    y, float *    z )  [static]

Definition at line 136 of file xsfplugin.C. References xsf_box::A, xsf_box::alpha, xsf_box::B, xsf_box::beta, xsf_box::C, xsf_box::cell, xsf_box::gamma, and M_PI_2. Referenced by read_xsf_structure, and read_xsf_timestep.

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Variable Documentation

xsf_keyword_t kw

Definition at line 67 of file xsfplugin.C. Referenced by open_xsf_read.

const char* name

Definition at line 66 of file xsfplugin.C. Referenced by append_prop_rule, atom_name_remove_underscores, atom_name_replace, babel16type_from_name, GEO_open_file_read, get_atom_radius, get_basis, get_bgf_fields, get_element_setup_ply, ReadPARM::get_parm_atom, get_pdb_fields, get_pqr_fields, Get_Property_Values, get_psf_atom, get_xbgf_fields, lookup_keyword, matches_rule_name, open_for_writing_ply, open_parm7_file, ReadPARM::open_parm_file, openbabel11type_from_name, ply_open_for_reading, read_car_structure_line, read_js_structure, read_mmtk_cdf_structure, read_tpr_structure, H5File::write_ds, write_js_structure, write_psf_structure, and writeAtomSite.

molfile_plugin_t plugin [static]

Definition at line 902 of file xsfplugin.C.

const { ... } xsf_aliases[] [static]

Referenced by lookup_keyword.

const char* xsf_symtab[] [static]

Initial value: { "(unknown keyword)", "#", "BEGIN_INFO", "END_INFO", "BEGIN_BLOCK_DATAGRID_2D", "END_BLOCK_DATAGRID_2D", "BEGIN_DATAGRID_2D", "END_DATAGRID_2D", "BEGIN_BLOCK_DATAGRID_3D", "END_BLOCK_DATAGRID_3D", "BEGIN_DATAGRID_3D", "END_DATAGRID_3D", "BEGIN_BLOCK_BANDGRID_3D", "END_BLOCK_BANDGRID_3D", "ATOMS", "ANIMSTEPS", "BAND", "MOLECULE", "POLYMER", "SLAB", "CRYSTAL", "PRIMVEC", "CONVVEC", "PRIMCOORD", "CONVCOORD" } Definition at line 34 of file xsfplugin.C. Referenced by lookup_keyword.

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