hoomdplugin.c File Reference

if (fabsf(box) > SMALL) {            \
    float tmp;                          \
    tmp = floorf(crd / box + 0.5f);     \
    p =  crd - tmp*box;                 \
    i = (int) tmp;                      \
  } else {                              \
    p = crd;                            \
    i = 0.0f;                           \
  }

ptr = (type *)calloc(count,sizeof(type)); \
  if (ptr == NULL) {                      \
                                          \
    PRINTERR;                             \
    return MOLFILE_ERROR;                 \
  }

SECTION_OPEN(tag,numatoms);             \
  for (i=0; i < numatoms; ++i)            \
    fprintf(data->fp,fmt, val);           \
  SECTION_CLOSE(tag)

strncpy(k, a[n],   sizeof(k)-1); make_lower(k);       \
  strncpy(v, a[n+1], sizeof(v)-1); make_lower(value)

vmdcon_printf(VMDCON_WARN, "hoomdplugin) ignoring unknown "       \
                " attribute %s='%s' for element %s\n", k, v, e);

 {
  "(none)", "hoomd_xml", "configuration", "box", 
  "position", "image", "velocity",               
  "type", "body", "mass", "charge", "diameter",  
  "bond", "angle", "dihedral", "improper",       
  "wall", "coord", "acceleration", "orientation",
  "(error)"                                      
}

Compounds
struct	hoomd_data_t
Defines
#define	THISPLUGIN plugin
#define	HOOMD_FORMAT_MAJV 1
#define	HOOMD_FORMAT_MINV 4
#define	SMALL 1.0e-7f /! arbitrary small number. "almost zero" /
#define	HOOMD_NONE 0 /*< undefined /
#define	HOOMD_XML 1 /*< toplevel tag /
#define	HOOMD_CONFIG 2 /*< timestep tag /
#define	HOOMD_BOX 3 /*< box dimensions tag /
#define	HOOMD_POS 4 /*< coordinates tag /
#define	HOOMD_IMAGE 5 /*< image counter tag /
#define	HOOMD_VEL 6 /*< velocities tag /
#define	HOOMD_TYPE 7 /*< atom type tag /
#define	HOOMD_BODY 8 /*< body number tag /
#define	HOOMD_MASS 9 /*< atom mass tag /
#define	HOOMD_CHARGE 10 /*< atom diameter tag /
#define	HOOMD_DIAMETER 11 /*< atom diameter tag /
#define	HOOMD_BOND 12 /*< bond section tag /
#define	HOOMD_ANGLE 13 /*< angle section tag /
#define	HOOMD_DIHEDRAL 14 /*< dihedral section tag /
#define	HOOMD_IMPROPER 15 /*< improper section tag /
#define	HOOMD_WALL 16 /*< wall description /
#define	HOOMD_COORD 17 /*< wall coordinate tag /
#define	HOOMD_ACCEL 18 /*< accelerations tag /
#define	HOOMD_ORIENT 19 /*< orientation tag /
#define	HOOMD_UNKNOWN 20 /*< unknown tag /
#define	HOOMD_NUMTAGS 21 /*< number of known tags /
#define	HOOMD_MAXDEPTH 5
#define	HOOMD_DEBUG 0
#define	PRINTERR (void)(0)
#define	SAFE_FREE(ptr) free(ptr); ptr=NULL
#define	SAFE_CALLOC(ptr, type, count)
#define	XML_ATTR_COPY(a, n, k, v)
#define	XML_UNK_ATTR(e, k, v)
#define	SECTION_OPEN(tag, num) fprintf(data->fp, "<%s num=\"%d\">\n", hoomd_tag_name[tag], num)
#define	SECTION_CLOSE(tag) fprintf(data->fp, "</%s>\n", hoomd_tag_name[tag])
#define	SECTION_WRITE_ATOMIC(tag, fmt, val)
#define	HOOMD_CONV_POS(crd, box, p, i)
Functions
void	make_lower (char *s)
int	addstring (char **list, const char key)
void	xml_new_tag (void data, const XML_Char elmt, const XML_Char **attr)
void	xml_end_tag (void data, const XML_Char elmt)
void	xml_data_block (void data, const XML_Char s, int len)
void	xml_comment (void data, const XML_Char s)
int	hoomd_parse_line (hoomd_data_t *data)
void *	open_hoomd_read (const char filename, const char filetype, int *natoms)
int	read_hoomd_structure (void mydata, int optflags, molfile_atom_t *atoms)
int	read_hoomd_bonds (void v, int nbonds, int fromptr, int toptr, float **bondorder)
int	read_hoomd_angles (void v, int numangles, int angles, double angleforces, int numdihedrals, int dihedrals, double dihedralforces, int numimpropers, int impropers, double improperforces, int numcterms, int cterms, int ctermcols, int ctermrows, double *ctermforces)
int	read_hoomd_timestep (void mydata, int natoms, molfile_timestep_t ts)
void	close_hoomd_read (void *mydata)
void *	open_hoomd_write (const char filename, const char filetype, int natoms)
int	write_hoomd_structure (void mydata, int optflags, const molfile_atom_t atoms)
int	write_hoomd_bonds (void v, int nbonds, int fromptr, int toptr, float bondorder)
int	write_hoomd_angles (void v, int numangles, const int angles, const double angleforces, int numdihedrals, const int dihedrals, const double dihedralforces, int numimpropers, const int impropers, const double improperforces, int numcterms, const int cterms, int ctermcols, int ctermrows, const double *ctermforces)
int	write_hoomd_timestep (void mydata, const molfile_timestep_t ts)
void	close_hoomd_write (void *mydata)
VMDPLUGIN_API int	VMDPLUGIN_init ()
VMDPLUGIN_API int	VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int	VMDPLUGIN_fini ()
Variables
const char *	hoomd_tag_name [HOOMD_NUMTAGS]
molfile_plugin_t	plugin
return	MOLFILE_SUCCESS

hoomdplugin.c File Reference

Compounds

Defines

Functions

Variables

Define Documentation

Function Documentation

Variable Documentation