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lmplugin.C File Reference

#include <cmath>
#include <cstdarg>
#include <cstdio>
#include <cstring>
#include <ctime>
#include <algorithm>
#include <exception>
#include <numeric>
#include <set>
#include <sstream>
#include <string>
#include <vector>
#include <hdf5.h>
#include <hdf5_hl.h>
#include "molfile_plugin.h"
#include "vmdconio.h"

Go to the source code of this file.

Namespaces

namespace  H5File_specialized

Compounds

class  Exception
class  H5Exception
class  H5File
class  LMPException
class  LMPlugin
struct  Timer

Defines

#define MAX_VMD_NAME   16
#define RDME_RADIUS_SCALE   0.1
#define TO_ANGSTROM   1e10
#define MAX_LMPEXC_MSG   256
#define H5_CALL_ASSIGN(val, call)
#define H5_CALL(call)

Typedefs

typedef unsigned char particle_int_t
typedef unsigned char site_int_t

Functions

void * open_read (const char *filename, const char *filetype, int *nAtom)
int read_structure (void *mydata, int *optflags, molfile_atom_t *atoms)
int read_bonds (void *mydata, int *nbonds, int **from, int **to, float **bondorder, int **bondtype, int *nbondtypes, char ***bondtypename)
int read_timestep (void *mydata, int nAtom, molfile_timestep_t *ts)
void close_read (void *mydata)
VMDPLUGIN_API int VMDPLUGIN_init ()
VMDPLUGIN_API int VMDPLUGIN_register (void *v, vmdplugin_register_cb cb)
VMDPLUGIN_API int VMDPLUGIN_fini ()

Define Documentation

#define H5_CALL (  call    ) 
 

Value:

do {                                                                                           \
        hid_t val;                                                                                 \
        H5_CALL_ASSIGN(val, (call));                                                               \
    } while (0)

Definition at line 113 of file lmplugin.C.

Referenced by H5File::close, H5File::get_dataset, H5File::get_group_listing, and H5File::write_ds.

#define H5_CALL_ASSIGN (  val,
call    ) 
 

Value:

do {                                                                                           \
        val = (call);                                                                              \
        if (val < 0) {                                                                             \
            throw H5Exception();                                                                   \
        }                                                                                          \
    } while (0)

Definition at line 105 of file lmplugin.C.

Referenced by H5File::get_dataset, H5File::get_group_listing, H5File::get_userblock, H5File::open, H5File::open_rdwr, and H5File::write_ds.

#define MAX_LMPEXC_MSG   256
 

Definition at line 65 of file lmplugin.C.

#define MAX_VMD_NAME   16
 

Definition at line 62 of file lmplugin.C.

#define RDME_RADIUS_SCALE   0.1
 

Definition at line 63 of file lmplugin.C.

#define TO_ANGSTROM   1e10
 

Definition at line 64 of file lmplugin.C.

Typedef Documentation

typedef unsigned char particle_int_t [static]
 

Definition at line 67 of file lmplugin.C.

Referenced by LMPlugin::read_timestep.

typedef unsigned char site_int_t [static]
 

Definition at line 68 of file lmplugin.C.

Referenced by LMPlugin::read_timestep.

Function Documentation

void close_read (  void *    mydata )  [static]
 

Definition at line 1087 of file lmplugin.C.

Referenced by VMDPLUGIN_init.

void* open_read (  const char *    filename,
const char *    filetype,
int *    nAtom
)  [static]
 

Definition at line 1019 of file lmplugin.C.

References LMPlugin::get_natoms.

Referenced by VMDPLUGIN_init.

int read_bonds (  void *    mydata,
int *    nbonds,
int **    from,
int **    to,
float **    bondorder,
int **    bondtype,
int *    nbondtypes,
char ***    bondtypename
)  [static]
 

Definition at line 1052 of file lmplugin.C.

References MOLFILE_ERROR, and LMPlugin::read_bonds.

Referenced by VMDPLUGIN_init.

int read_structure (  void *    mydata,
int *    optflags,
molfile_atom_t *    atoms
)  [static]
 

Definition at line 1037 of file lmplugin.C.

References MOLFILE_ERROR, and LMPlugin::read_structure.

Referenced by VMDPLUGIN_init.

int read_timestep (  void *    mydata,
int    nAtom,
molfile_timestep_t *    ts
)  [static]
 

Definition at line 1072 of file lmplugin.C.

References MOLFILE_ERROR, and LMPlugin::read_timestep.

Referenced by VMDPLUGIN_init.

VMDPLUGIN_API int VMDPLUGIN_fini (  void    ) 
 

Definition at line 1123 of file lmplugin.C.

References VMDPLUGIN_SUCCESS.

VMDPLUGIN_API int VMDPLUGIN_init (  void    ) 
 

Definition at line 1094 of file lmplugin.C.

References close_read, MOLFILE_PLUGIN_TYPE, open_read, read_bonds, read_structure, read_timestep, vmdplugin_ABIVERSION, VMDPLUGIN_SUCCESS, and VMDPLUGIN_THREADSAFE.

VMDPLUGIN_API int VMDPLUGIN_register (  void *    v,
vmdplugin_register_cb    cb
) 
 

Definition at line 1115 of file lmplugin.C.

References vmdplugin_register_cb, and VMDPLUGIN_SUCCESS.

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