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Merge branch 'unstable' of https://github.com/ketankhare/lammps into small-fixes-and-updates

This commit is contained in:
Axel Kohlmeyer 2017-04-18 11:20:23 -04:00
parent 4bad52f30c 3d3d1061d3
commit 73c210b665
3 changed files with 206 additions and 194 deletions
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3
src/USER-MOLFILE/README
View File

@ -28,8 +28,7 @@ taken from. These header files can be found inside the VMD
installation tree under: "plugins/include".
For convenience, this package includes a set of header files that is
compatible with VMD 1.9 and 1.9.1 (the current version in June 2012)
and should be compilable with VMD versions back to about version 1.8.4
compatible with VMD 1.9.3 (the current version in April 2017)
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.

339
src/USER-MOLFILE/molfile_plugin.h
View File

@ -11,14 +11,14 @@
*
* $RCSfile: molfile_plugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.103 $ $Date: 2011/03/05 03:56:11 $
* $Revision: 1.108 $ $Date: 2016/02/26 03:17:01 $
*
***************************************************************************/
/** @file
/** @file
* API for C extensions to define a way to load structure, coordinate,
* trajectory, and volumetric data files
*/
* trajectory, and volumetric data files
*/
#ifndef MOL_FILE_PLUGIN_H
#define MOL_FILE_PLUGIN_H
@ -60,6 +60,21 @@ typedef ssize_t molfile_ssize_t; /**< for frame counts */
#define MOLFILE_MAXWAVEPERTS 25 /**< maximum number of wavefunctions
* per timestep */
/**
* Hard-coded direct-I/O page size constants for use by both VMD
* and the plugins that want to use direct, unbuffered I/O for high
* performance with SSDs etc. We use two constants to define the
* range of hardware page sizes that we can support, so that we can
* add support for larger 8KB or 16KB page sizes in the future
* as they become more prevalent in high-end storage systems.
*
* At present, VMD uses a hard-coded 4KB page size to reduce memory
* fragmentation, but these constants will make it easier to enable the
* use of larger page sizes in the future if it becomes necessary.
*/
#define MOLFILE_DIRECTIO_MIN_BLOCK_SIZE 4096
#define MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096
/**
* File level comments, origin information, and annotations.
@ -74,16 +89,16 @@ typedef struct {
} molfile_metadata_t;
/*
* Struct for specifying atoms in a molecular structure. The first
* six components are required, the rest are optional and their presence is
/*
* Struct for specifying atoms in a molecular structure. The first
* six components are required, the rest are optional and their presence is
* indicating by setting the corresponding bit in optsflag. When omitted,
* the application (for read_structure) or plugin (for write_structure)
* must be able to supply default values if the missing parameters are
* the application (for read_structure) or plugin (for write_structure)
* must be able to supply default values if the missing parameters are
* part of its internal data structure.
* Note that it is not possible to specify coordinates with this structure.
* This is intentional; all coordinate I/O is done with the read_timestep and
* write_timestep functions.
* This is intentional; all coordinate I/O is done with the read_timestep and
* write_timestep functions.
*/
/**
@ -96,8 +111,17 @@ typedef struct {
char resname[8]; /**< required residue name string */
int resid; /**< required integer residue ID */
char segid[8]; /**< required segment name string, or "" */
#if 0 && vmdplugin_ABIVERSION > 17
/* The new PDB file formats allows for much larger structures, */
/* which can therefore require longer chain ID strings. The */
/* new PDBx/mmCIF file formats do not have length limits on */
/* fields, so PDB chains could be arbitrarily long strings */
/* in such files. At present, we know we need at least 3-char */
/* chains for existing PDBx/mmCIF files. */
char chain[4]; /**< required chain name, or "" */
#else
char chain[2]; /**< required chain name, or "" */
#endif
/* rest are optional; use optflags to specify what's present */
char altloc[2]; /**< optional PDB alternate location code */
char insertion[2]; /**< optional PDB insertion code */
@ -107,6 +131,23 @@ typedef struct {
float charge; /**< optional charge value */
float radius; /**< optional radius value */
int atomicnumber; /**< optional element atomic number */
#if 0
char complex[16];
char assembly[16];
int qmregion;
int qmregionlink;
int qmlayer;
int qmlayerlink;
int qmfrag;
int qmfraglink;
string qmecp;
int qmadapt;
int qmect; /**< boolean */
int qmparam;
int autoparam;
#endif
#if defined(DESRES_CTNUMBER)
int ctnumber; /**< mae ct block, 0-based, including meta */
#endif
@ -128,7 +169,7 @@ typedef struct {
#define MOLFILE_CTNUMBER 0x0200 /**< ctnumber provided */
#endif
#define MOLFILE_BADOPTIONS 0xFFFFFFFF /**< Detect badly behaved plugins */
/*@}*/
/*@{*/
@ -140,38 +181,32 @@ typedef struct {
#define MOLFILE_QMTS_SCFITER 0x0002
/*@}*/
#if vmdplugin_ABIVERSION > 10
typedef struct molfile_timestep_metadata {
unsigned int count; /**< total # timesteps; -1 if unknown */
unsigned int avg_bytes_per_timestep; /** bytes per timestep */
int has_velocities; /**< if timesteps have velocities */
} molfile_timestep_metadata_t;
#endif
/*
* Per-timestep atom coordinates and periodic cell information
*/
*/
typedef struct {
float *coords; /**< coordinates of all atoms, arranged xyzxyzxyz */
#if vmdplugin_ABIVERSION > 10
float *velocities; /**< space for velocities of all atoms; same layout */
/**< NULL unless has_velocities is set */
#endif
/*@{*/
/*@{*/
/**
* 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
*/
float A, B, C, alpha, beta, gamma;
/*@}*/
*/
float A, B, C, alpha, beta, gamma;
/*@}*/
#if vmdplugin_ABIVERSION > 10
double physical_time; /**< physical time point associated with this frame */
#endif
#if defined(DESRES_READ_TIMESTEP2)
/* HACK to support generic trajectory information */
@ -188,7 +223,7 @@ typedef struct {
/**
* Metadata for volumetric datasets, read initially and used for subsequent
* memory allocations and file loading.
* memory allocations and file loading.
*/
typedef struct {
char dataname[256]; /**< name of volumetric data set */
@ -198,29 +233,48 @@ typedef struct {
* x/y/z axis:
* These the three cell sides, providing both direction and length
* (not unit vectors) for the x, y, and z axes. In the simplest
* case, these would be <size,0,0> <0,size,0> and <0,0,size) for
* case, these would be <size,0,0> <0,size,0> and <0,0,size) for
* an orthogonal cubic volume set. For other cell shapes these
* axes can be oriented non-orthogonally, and the parallelpiped
* may have different side lengths, not just a cube/rhombus.
*/
float xaxis[3]; /**< direction (and length) for X axis */
float xaxis[3]; /**< direction (and length) for X axis */
float yaxis[3]; /**< direction (and length) for Y axis */
float zaxis[3]; /**< direction (and length) for Z axis */
/*
* x/y/z size:
* x/y/z size:
* Number of grid cells along each axis. This is _not_ the
* physical size of the box, this is the number of voxels in each
* direction, independent of the shape of the volume set.
* direction, independent of the shape of the volume set.
*/
int xsize; /**< number of grid cells along the X axis */
int ysize; /**< number of grid cells along the Y axis */
int zsize; /**< number of grid cells along the Z axis */
int xsize; /**< number of grid cells along the X axis */
int ysize; /**< number of grid cells along the Y axis */
int zsize; /**< number of grid cells along the Z axis */
int has_color; /**< flag indicating presence of voxel color data */
#if vmdplugin_ABIVERSION > 16
int has_scalar; /**< flag indicating presence of scalar volume */
int has_gradient; /**< flag indicating presence of vector volume */
int has_variance; /**< flag indicating presence of variance map */
#endif
int has_color; /**< flag indicating presence of voxel color data */
} molfile_volumetric_t;
#if vmdplugin_ABIVERSION > 16
/**
* Volumetric dataset read/write structure with both flag/parameter sets
* and VMD-allocated pointers for fields to be used by the plugin.
*/
typedef struct {
int setidx; /**< volumetric dataset index to load/save */
float *scalar; /**< scalar density/potential field data */
float *gradient; /**< gradient vector field */
float *variance; /**< variance map indicating signal/noise */
float *rgb3f; /**< RGB floating point color texture map */
unsigned char *rgb3u; /**< RGB unsigned byte color texture map */
} molfile_volumetric_readwrite_t;
#endif
/**************************************************************
@ -231,9 +285,6 @@ typedef struct {
**************************************************************
**************************************************************/
#if vmdplugin_ABIVERSION > 9
/* macros for the convergence status of a QM calculation. */
#define MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */
#define MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */
@ -297,10 +348,10 @@ typedef struct {
/**
* QM run info. Parameters that stay unchanged during a single file.
*/
*/
typedef struct {
int nproc; /**< number of processors used. */
int memory; /**< amount of memory used in Mbyte. */
int memory; /**< amount of memory used in Mbyte. */
int runtype; /**< flag indicating the calculation method. */
int scftype; /**< SCF type: RHF, UHF, ROHF, GVB or MCSCF wfn. */
int status; /**< indicates wether SCF and geometry optimization
@ -333,9 +384,9 @@ typedef struct {
* array size = 2*num_basis_funcs
* The basis must NOT be normalized. */
int *atomic_number; /**< atomic numbers (chem. element) of atoms in basis set */
int *angular_momentum; /**< 3 ints per wave function coefficient do describe the
int *angular_momentum; /**< 3 ints per wave function coefficient do describe the
* cartesian components of the angular momentum.
* E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}.
* E.g. S={0 0 0}, Px={1 0 0}, Dxy={1 1 0}, or Fyyz={0 2 1}.
*/
int *shell_types; /**< type for each shell in basis */
} molfile_qm_basis_t;
@ -409,9 +460,9 @@ enum molfile_qm_wavefunc_type {
MOLFILE_WAVE_MCSCFNAT, MOLFILE_WAVE_MCSCFOPT,
MOLFILE_WAVE_CINATUR,
MOLFILE_WAVE_PIPEK, MOLFILE_WAVE_BOYS, MOLFILE_WAVE_RUEDEN,
MOLFILE_WAVE_NAO, MOLFILE_WAVE_PNAO, MOLFILE_WAVE_NHO,
MOLFILE_WAVE_PNHO, MOLFILE_WAVE_NBO, MOLFILE_WAVE_PNBO,
MOLFILE_WAVE_PNLMO, MOLFILE_WAVE_NLMO, MOLFILE_WAVE_MOAO,
MOLFILE_WAVE_NAO, MOLFILE_WAVE_PNAO, MOLFILE_WAVE_NHO,
MOLFILE_WAVE_PNHO, MOLFILE_WAVE_NBO, MOLFILE_WAVE_PNBO,
MOLFILE_WAVE_PNLMO, MOLFILE_WAVE_NLMO, MOLFILE_WAVE_MOAO,
MOLFILE_WAVE_NATO, MOLFILE_WAVE_UNKNOWN
};
@ -442,7 +493,7 @@ typedef struct molfile_qm_timestep_metadata {
int has_orben_per_wavef[MOLFILE_MAXWAVEPERTS]; /**< orbital energy flags */
int has_occup_per_wavef[MOLFILE_MAXWAVEPERTS]; /**< orbital occupancy flags */
int num_wavef ; /**< # wavefunctions in this ts */
int wavef_size; /**< size of one wavefunction
int wavef_size; /**< size of one wavefunction
* (# of gaussian basis fctns) */
int num_charge_sets; /**< # of charge values per atom */
} molfile_qm_timestep_metadata_t;
@ -485,8 +536,6 @@ typedef struct {
} molfile_qm_timestep_t;
#endif
/**************************************************************
**************************************************************/
@ -498,14 +547,14 @@ typedef struct {
* from graphics file reader plugins.
*/
enum molfile_graphics_type {
MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
MOLFILE_POINT, MOLFILE_TRIANGLE, MOLFILE_TRINORM, MOLFILE_NORMS,
MOLFILE_LINE, MOLFILE_CYLINDER, MOLFILE_CAPCYL, MOLFILE_CONE,
MOLFILE_SPHERE, MOLFILE_TEXT, MOLFILE_COLOR, MOLFILE_TRICOLOR
};
/**
* Individual graphics object/element data
*/
*/
typedef struct {
int type; /* One of molfile_graphics_type */
int style; /* A general style parameter */
@ -521,13 +570,13 @@ typedef struct {
type data style size
---- ---- ----- ----
point x, y, z pixel size
triangle x1,y1,z1,x2,y2,z2,x3,y3,z3
trinorm x1,y1,z1,x2,y2,z2,x3,y3,z3
triangle x1,y1,z1,x2,y2,z2,x3,y3,z3
trinorm x1,y1,z1,x2,y2,z2,x3,y3,z3
the next array element must be NORMS
tricolor x1,y1,z1,x2,y2,z2,x3,y3,z3
tricolor x1,y1,z1,x2,y2,z2,x3,y3,z3
the next array elements must be NORMS
the following element must be COLOR, with three RGB triples
norms x1,y1,z1,x2,y2,z2,x3,y3,z3
norms x1,y1,z1,x2,y2,z2,x3,y3,z3
line x1,y1,z1,x2,y2,z2 0=solid pixel width
1=stippled
cylinder x1,y1,z1,x2,y2,z2 resolution radius
@ -541,41 +590,41 @@ color r, g, b
/**
* Main file reader API. Any function in this struct may be NULL
* if not implemented by the plugin; the application checks this to determine
* what functionality is present in the plugin.
*/
* what functionality is present in the plugin.
*/
typedef struct {
/**
* Required header
* Required header
*/
vmdplugin_HEAD
/**
* Filename extension for this file type. May be NULL if no filename
* Filename extension for this file type. May be NULL if no filename
* extension exists and/or is known. For file types that match several
* common extensions, list them in a comma separated list such as:
* "pdb,ent,foo,bar,baz,ban"
* The comma separated list will be expanded when filename extension matching
* is performed. If multiple plugins solicit the same filename extensions,
* the one that lists the extension earliest in its list is selected. In the
* the one that lists the extension earliest in its list is selected. In the
* case of a "tie", the first one tried/checked "wins".
*/
const char *filename_extension;
/**
* Try to open the file for reading. Return an opaque handle, or NULL on
* failure. Set the number of atoms; if the number of atoms cannot be
* determined, set natoms to MOLFILE_NUMATOMS_UNKNOWN.
* failure. Set the number of atoms; if the number of atoms cannot be
* determined, set natoms to MOLFILE_NUMATOMS_UNKNOWN.
* Filetype should be the name under which this plugin was registered;
* this is provided so that plugins can provide the same function pointer
* to handle multiple file types.
*/
void *(* open_file_read)(const char *filepath, const char *filetype,
void *(* open_file_read)(const char *filepath, const char *filetype,
int *natoms);
/**
* Read molecular structure from the given file handle. atoms is allocated
* by the caller and points to space for natoms.
* On success, place atom information in the passed-in pointer.
* On success, place atom information in the passed-in pointer.
* optflags specifies which optional fields in the atoms will be set by
* the plugin.
*/
@ -587,15 +636,15 @@ typedef struct {
* Each unique bond should be specified only once, so file formats that list
* bonds twice will need post-processing before the results are returned to
* the caller.
* If the plugin provides bond information, but the file loaded doesn't
* If the plugin provides bond information, but the file loaded doesn't
* actually contain any bond info, the nbonds parameter should be
* set to 0 and from/to should be set to NULL to indicate that no bond
* information was actually present, and automatic bond search should be
* performed.
* performed.
*
* If the plugin provides bond order information, the bondorder array
* will contain the bond order for each from/to pair. If not, the bondorder
* pointer should be set to NULL, in which case the caller will provide a
* pointer should be set to NULL, in which case the caller will provide a
* default bond order value of 1.0.
*
* If the plugin provides bond type information, the bondtype array
@ -606,27 +655,23 @@ typedef struct {
* and consistency checking.
*
* These arrays must be freed by the plugin in the close_file_read function.
* This function can be called only after read_structure().
* Return MOLFILE_SUCCESS if no errors occur.
* This function can be called only after read_structure().
* Return MOLFILE_SUCCESS if no errors occur.
*/
#if vmdplugin_ABIVERSION > 14
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
int **bondtype, int *nbondtypes, char ***bondtypename);
#else
int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder);
#endif
/**
* XXX this function will be augmented and possibly superceded by a
* XXX this function will be augmented and possibly superceded by a
* new QM-capable version named read_timestep(), when finished.
*
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
* MOLFILE_EOF on EOF. If the molfile_timestep_t argument is NULL, then
* the frame should be skipped. Otherwise, the application must prepare
* molfile_timestep_t by allocating space in coords for the corresponding
* number of coordinates.
* The natoms parameter exists because some coordinate file formats
* (like CRD) cannot determine for themselves how many atoms are in a
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
* MOLFILE_EOF on EOF. If the molfile_timestep_t argument is NULL, then
* the frame should be skipped. Otherwise, the application must prepare
* molfile_timestep_t by allocating space in coords for the corresponding
* number of coordinates.
* The natoms parameter exists because some coordinate file formats
* (like CRD) cannot determine for themselves how many atoms are in a
* timestep; the app must therefore obtain this information elsewhere
* and provide it to the plugin.
*/
@ -636,16 +681,16 @@ typedef struct {
* Close the file and release all data. The handle cannot be reused.
*/
void (* close_file_read)(void *);
/**
* Open a coordinate file for writing using the given header information.
* Return an opaque handle, or NULL on failure. The application must
* specify the number of atoms to be written.
* specify the number of atoms to be written.
* filetype should be the name under which this plugin was registered.
*/
void *(* open_file_write)(const char *filepath, const char *filetype,
void *(* open_file_write)(const char *filepath, const char *filetype,
int natoms);
/**
* Write structure information. Return success.
*/
@ -653,12 +698,12 @@ typedef struct {
/**
* Write a timestep to the coordinate file. Return MOLFILE_SUCCESS if no
* errors occur. If the file contains structure information in each
* timestep (like a multi-entry PDB), it will have to cache the information
* errors occur. If the file contains structure information in each
* timestep (like a multi-entry PDB), it will have to cache the information
* from the initial calls from write_structure.
*/
int (* write_timestep)(void *, const molfile_timestep_t *);
/**
* Close the file and release all data. The handle cannot be reused.
*/
@ -671,24 +716,27 @@ typedef struct {
* the plugin and should be freed by close_file_read(). The application
* may call this function any number of times.
*/
int (* read_volumetric_metadata)(void *, int *nsets,
int (* read_volumetric_metadata)(void *, int *nsets,
molfile_volumetric_t **metadata);
/**
* Read the specified volumetric data set into the space pointed to by
* datablock. The set is specified with a zero-based index. The space
/**
* Read the specified volumetric data set into the space pointed to by
* datablock. The set is specified with a zero-based index. The space
* allocated for the datablock must be equal to
* xsize * ysize * zsize. No space will be allocated for colorblock
* xsize * ysize * zsize. No space will be allocated for colorblock
* unless has_color is nonzero; in that case, colorblock should be
* filled in with three RGB floats per datapoint.
*/
int (* read_volumetric_data)(void *, int set, float *datablock,
int (* read_volumetric_data)(void *, int set, float *datablock,
float *colorblock);
#if vmdplugin_ABIVERSION > 16
int (* read_volumetric_data_ex)(void *, molfile_volumetric_readwrite_t *v);
#endif
/**
* Read raw graphics data stored in this file. Return the number of data
* elements and the data itself as an array of molfile_graphics_t in the
* pointer provided by the application. The plugin is responsible for
* elements and the data itself as an array of molfile_graphics_t in the
* pointer provided by the application. The plugin is responsible for
* freeing the data when the file is closed.
*/
int (* read_rawgraphics)(void *, int *nelem, const molfile_graphics_t **data);
@ -698,19 +746,19 @@ typedef struct {
* came from, what the accession code for the database is, textual remarks
* and other notes pertaining to the contained structure/trajectory/volume
* and anything else that's informative at the whole file level.
*/
*/
int (* read_molecule_metadata)(void *, molfile_metadata_t **metadata);
/**
* Write bond information for the molecule. The arrays from
* and to point to the (one-based) indices of bonded atoms.
* Each unique bond will be specified only once by the caller.
* File formats that list bonds twice will need to emit both the
* Each unique bond will be specified only once by the caller.
* File formats that list bonds twice will need to emit both the
* from/to and to/from versions of each.
* This function must be called before write_structure().
* This function must be called before write_structure().
*
* Like the read_bonds() routine, the bondorder pointer is set to NULL
* if the caller doesn't have such information, in which case the
* if the caller doesn't have such information, in which case the
* plugin should assume a bond order of 1.0 if the file format requires
* bond order information.
*
@ -721,76 +769,47 @@ typedef struct {
* scheme is different from the index numbers.
* if the pointers are set to NULL, then this information is not available.
* bondtypenames can only be used of bondtypes is also given.
* Return MOLFILE_SUCCESS if no errors occur.
* Return MOLFILE_SUCCESS if no errors occur.
*/
#if vmdplugin_ABIVERSION > 14
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
int *bondtype, int nbondtypes, char **bondtypename);
#else
int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
#endif
#if vmdplugin_ABIVERSION > 9
/**
* Write the specified volumetric data set into the space pointed to by
* Write the specified volumetric data set into the space pointed to by
* datablock. The * allocated for the datablock must be equal to
* xsize * ysize * zsize. No space will be allocated for colorblock
* xsize * ysize * zsize. No space will be allocated for colorblock
* unless has_color is nonzero; in that case, colorblock should be
* filled in with three RGB floats per datapoint.
*/
int (* write_volumetric_data)(void *, molfile_volumetric_t *metadata,
float *datablock, float *colorblock);
#if vmdplugin_ABIVERSION > 16
int (* write_volumetric_data_ex)(void *, molfile_volumetric_t *metadata,
molfile_volumetric_readwrite_t *v);
#endif
#if vmdplugin_ABIVERSION > 15
/**
/**
* Read in Angles, Dihedrals, Impropers, and Cross Terms and optionally types.
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
*/
int (* read_angles)(void *handle, int *numangles, int **angles, int **angletypes,
int *numangletypes, char ***angletypenames, int *numdihedrals,
int **dihedrals, int **dihedraltypes, int *numdihedraltypes,
char ***dihedraltypenames, int *numimpropers, int **impropers,
char ***dihedraltypenames, int *numimpropers, int **impropers,
int **impropertypes, int *numimpropertypes, char ***impropertypenames,
int *numcterms, int **cterms, int *ctermcols, int *ctermrows);
/**
/**
* Write out Angles, Dihedrals, Impropers, and Cross Terms
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
*/
int (* write_angles)(void *handle, int numangles, const int *angles, const int *angletypes,
int numangletypes, const char **angletypenames, int numdihedrals,
const int *dihedrals, const int *dihedraltypes, int numdihedraltypes,
const char **dihedraltypenames, int numimpropers,
const char **dihedraltypenames, int numimpropers,
const int *impropers, const int *impropertypes, int numimpropertypes,
const char **impropertypenames, int numcterms, const int *cterms,
const char **impropertypenames, int numcterms, const int *cterms,
int ctermcols, int ctermrows);
#else
/**
* Read in Angles, Dihedrals, Impropers, and Cross Terms
* Forces are in Kcal/mol
* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
* as a 2-D matrix)
*/
int (* read_angles)(void *,
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);
/**
* Write out Angles, Dihedrals, Impropers, and Cross Terms
* Forces are in Kcal/mol
* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
* as a 2-D matrix)
*/
int (* write_angles)(void *,
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);
#endif
/**
@ -798,7 +817,7 @@ typedef struct {
* QM datasets in this file.
*
* The metadata are the sizes of the QM related data structure
* arrays that will be populated by the plugin when
* arrays that will be populated by the plugin when
* read_qm_rundata() is called. Since the allocation of these
* arrays is done by VMD rather than the plugin, VMD needs to
* know the sizes beforehand. Consequently read_qm_metadata()
@ -811,7 +830,7 @@ typedef struct {
* Read timestep independent QM data.
*
* Typical data that are defined only once per trajectory are
* general info about the calculation (such as the used method),
* general info about the calculation (such as the used method),
* the basis set and normal modes.
* The data structures to be populated must have been allocated
* before by VMD according to sizes obtained through
@ -821,32 +840,27 @@ typedef struct {
/**
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
* Read the next timestep from the file. Return MOLFILE_SUCCESS, or
* MOLFILE_EOF on EOF. If the molfile_timestep_t or molfile_qm_metadata_t
* arguments are NULL, then the coordinate or qm data should be skipped.
* Otherwise, the application must prepare molfile_timestep_t and
* molfile_qm_timestep_t by allocating space for the corresponding
* arguments are NULL, then the coordinate or qm data should be skipped.
* Otherwise, the application must prepare molfile_timestep_t and
* molfile_qm_timestep_t by allocating space for the corresponding
* number of coordinates, orbital wavefunction coefficients, etc.
* Since it is common for users to want to load only the final timestep
* Since it is common for users to want to load only the final timestep
* data from a QM run, the application may provide any combination of
* valid, or NULL pointers for the molfile_timestep_t and
* valid, or NULL pointers for the molfile_timestep_t and
* molfile_qm_timestep_t parameters, depending on what information the
* user is interested in.
* The natoms and qm metadata parameters exist because some file formats
* cannot determine for themselves how many atoms etc are in a
* The natoms and qm metadata parameters exist because some file formats
* cannot determine for themselves how many atoms etc are in a
* timestep; the app must therefore obtain this information elsewhere
* and provide it to the plugin.
*/
int (* read_timestep)(void *, int natoms, molfile_timestep_t *,
molfile_qm_metadata_t *, molfile_qm_timestep_t *);
#endif
#if vmdplugin_ABIVERSION > 10
int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
#endif
#if vmdplugin_ABIVERSION > 11
int (* read_qm_timestep_metadata)(void *, molfile_qm_timestep_metadata_t *);
#endif
#if defined(DESRES_READ_TIMESTEP2)
/**
@ -864,7 +878,6 @@ typedef struct {
double * times );
#endif
#if vmdplugin_ABIVERSION > 13
/**
* Console output, READ-ONLY function pointer.
* Function pointer that plugins can use for printing to the host
@ -883,8 +896,8 @@ typedef struct {
* application-provided services
*/
int (* cons_fputs)(const int, const char*);
#endif
} molfile_plugin_t;
#endif

58
src/USER-MOLFILE/vmdplugin.h
View File

@ -11,26 +11,26 @@
*
* $RCSfile: vmdplugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.32 $ $Date: 2009/02/24 05:12:35 $
* $Revision: 1.33 $ $Date: 2015/10/29 05:10:54 $
*
***************************************************************************/
/** @file
* This header must be included by every VMD plugin library. It defines the
* API for every plugin so that VMD can organize the plugins it finds.
* API for every plugin so that VMD can organize the plugins it finds.
*/
#ifndef VMD_PLUGIN_H
#define VMD_PLUGIN_H
/*
/*
* Preprocessor tricks to make it easier for us to redefine the names of
* functions when building static plugins.
*/
#if !defined(VMDPLUGIN)
/**
* macro defining VMDPLUGIN if it hasn't already been set to the name of
/**
* macro defining VMDPLUGIN if it hasn't already been set to the name of
* a static plugin that is being compiled. This is the catch-all case.
*/
#define VMDPLUGIN vmdplugin
@ -38,11 +38,11 @@
/** concatenation macro, joins args x and y together as a single string */
#define xcat(x, y) cat(x, y)
/** concatenation macro, joins args x and y together as a single string */
#define cat(x, y) x ## y
#define cat(x, y) x ## y
/*
* macros to correctly define plugin function names depending on whether
* the plugin is being compiled for static linkage or dynamic loading.
* macros to correctly define plugin function names depending on whether
* the plugin is being compiled for static linkage or dynamic loading.
* When compiled for static linkage, each plugin needs to have unique
* function names for all of its entry points. When compiled for dynamic
* loading, the plugins must name their entry points consistently so that
@ -59,13 +59,13 @@
/** "WIN32" is defined on both WIN32 and WIN64 platforms... */
#if (defined(WIN32))
#if (defined(WIN32))
#define WIN32_LEAN_AND_MEAN
#include <windows.h>
#if !defined(STATIC_PLUGIN)
#if defined(VMDPLUGIN_EXPORTS)
/**
/**
* Only define DllMain for plugins, not in VMD or in statically linked plugins
* VMDPLUGIN_EXPORTS is only defined when compiling dynamically loaded plugins
*/
@ -86,7 +86,7 @@ BOOL APIENTRY DllMain( HANDLE hModule,
#endif /* ! STATIC_PLUGIN */
#else
/** If we're not compiling on Windows, then this macro is defined empty */
#define VMDPLUGIN_API
#define VMDPLUGIN_API
#endif
/** define plugin linkage correctly for both C and C++ based plugins */
@ -96,13 +96,13 @@ BOOL APIENTRY DllMain( HANDLE hModule,
#define VMDPLUGIN_EXTERN extern VMDPLUGIN_API
#endif /* __cplusplus */
/*
* Plugin API functions start here
/*
* Plugin API functions start here
*/
/**
* Init routine: called the first time the library is loaded by the
/**
* Init routine: called the first time the library is loaded by the
* application and before any other API functions are referenced.
* Return 0 on success.
*/
@ -110,15 +110,15 @@ VMDPLUGIN_EXTERN int VMDPLUGIN_init(void);
/**
* Macro for creating a struct header used in all plugin structures.
*
* This header should be placed at the top of every plugin API definition
*
* This header should be placed at the top of every plugin API definition
* so that it can be treated as a subtype of the base plugin type.
*
* abiversion: Defines the ABI for the base plugin type (not for other plugins)
* type: A string descriptor of the plugin type.
* name: A name for the plugin.
* author: A string identifier, possibly including newlines.
* Major and minor version.
* Major and minor version.
* is_reentrant: Whether this library can be run concurrently with itself.
*/
#define vmdplugin_HEAD \
@ -129,12 +129,12 @@ VMDPLUGIN_EXTERN int VMDPLUGIN_init(void);
const char *author; \
int majorv; \
int minorv; \
int is_reentrant;
int is_reentrant;
/**
/**
* Typedef for generic plugin header, individual plugins can
* make their own structures as long as the header info remains
* the same as the generic plugin header, most easily done by
* make their own structures as long as the header info remains
* the same as the generic plugin header, most easily done by
* using the vmdplugin_HEAD macro.
*/
typedef struct {
@ -144,7 +144,7 @@ typedef struct {
/**
* Use this macro to initialize the abiversion member of each plugin
*/
#define vmdplugin_ABIVERSION 16
#define vmdplugin_ABIVERSION 17
/*@{*/
/** Use this macro to indicate a plugin's thread-safety at registration time */
@ -158,7 +158,7 @@ typedef struct {
#define VMDPLUGIN_ERROR -1
/*@}*/
/**
/**
* Function pointer typedef for register callback functions
*/
typedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
@ -175,16 +175,16 @@ typedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
VMDPLUGIN_EXTERN int VMDPLUGIN_register(void *, vmdplugin_register_cb);
/**
* Allow the library to register Tcl extensions.
* Allow the library to register Tcl extensions.
* This API is optional; if found by dlopen, it will be called after first
* calling init and register.
* calling init and register.
*/
VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl(void *, void *tcl_interp,
VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl(void *, void *tcl_interp,
vmdplugin_register_cb);
/**
* The Fini method is called when the application will no longer use
* any plugins in the library.
* The Fini method is called when the application will no longer use
* any plugins in the library.
*/
VMDPLUGIN_EXTERN int VMDPLUGIN_fini(void);