forked from lijiext/lammps
Updated to 1.108 from 1.103
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ketankhare
GitHub
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@ -11,7 +11,7 @@
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*
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* $RCSfile: molfile_plugin.h,v $
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* $Author: johns $ $Locker: $ $State: Exp $
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* $Revision: 1.103 $ $Date: 2011/03/05 03:56:11 $
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* $Revision: 1.108 $ $Date: 2016/02/26 03:17:01 $
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*
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***************************************************************************/
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@ -60,6 +60,21 @@ typedef ssize_t molfile_ssize_t; /**< for frame counts */
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#define MOLFILE_MAXWAVEPERTS 25 /**< maximum number of wavefunctions
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* per timestep */
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/**
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* Hard-coded direct-I/O page size constants for use by both VMD
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* and the plugins that want to use direct, unbuffered I/O for high
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* performance with SSDs etc. We use two constants to define the
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* range of hardware page sizes that we can support, so that we can
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* add support for larger 8KB or 16KB page sizes in the future
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* as they become more prevalent in high-end storage systems.
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*
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* At present, VMD uses a hard-coded 4KB page size to reduce memory
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* fragmentation, but these constants will make it easier to enable the
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* use of larger page sizes in the future if it becomes necessary.
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*/
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#define MOLFILE_DIRECTIO_MIN_BLOCK_SIZE 4096
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#define MOLFILE_DIRECTIO_MAX_BLOCK_SIZE 4096
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/**
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* File level comments, origin information, and annotations.
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@ -96,8 +111,17 @@ typedef struct {
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char resname[8]; /**< required residue name string */
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int resid; /**< required integer residue ID */
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char segid[8]; /**< required segment name string, or "" */
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#if 0 && vmdplugin_ABIVERSION > 17
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/* The new PDB file formats allows for much larger structures, */
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/* which can therefore require longer chain ID strings. The */
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/* new PDBx/mmCIF file formats do not have length limits on */
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/* fields, so PDB chains could be arbitrarily long strings */
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/* in such files. At present, we know we need at least 3-char */
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/* chains for existing PDBx/mmCIF files. */
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char chain[4]; /**< required chain name, or "" */
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#else
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char chain[2]; /**< required chain name, or "" */
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#endif
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/* rest are optional; use optflags to specify what's present */
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char altloc[2]; /**< optional PDB alternate location code */
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char insertion[2]; /**< optional PDB insertion code */
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@ -107,6 +131,23 @@ typedef struct {
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float charge; /**< optional charge value */
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float radius; /**< optional radius value */
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int atomicnumber; /**< optional element atomic number */
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#if 0
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char complex[16];
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char assembly[16];
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int qmregion;
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int qmregionlink;
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int qmlayer;
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int qmlayerlink;
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int qmfrag;
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int qmfraglink;
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string qmecp;
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int qmadapt;
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int qmect; /**< boolean */
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int qmparam;
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int autoparam;
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#endif
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#if defined(DESRES_CTNUMBER)
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int ctnumber; /**< mae ct block, 0-based, including meta */
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#endif
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@ -140,23 +181,19 @@ typedef struct {
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#define MOLFILE_QMTS_SCFITER 0x0002
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/*@}*/
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#if vmdplugin_ABIVERSION > 10
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typedef struct molfile_timestep_metadata {
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unsigned int count; /**< total # timesteps; -1 if unknown */
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unsigned int avg_bytes_per_timestep; /** bytes per timestep */
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int has_velocities; /**< if timesteps have velocities */
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} molfile_timestep_metadata_t;
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#endif
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/*
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* Per-timestep atom coordinates and periodic cell information
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*/
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typedef struct {
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float *coords; /**< coordinates of all atoms, arranged xyzxyzxyz */
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#if vmdplugin_ABIVERSION > 10
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float *velocities; /**< space for velocities of all atoms; same layout */
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/**< NULL unless has_velocities is set */
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#endif
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/*@{*/
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/**
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@ -169,9 +206,7 @@ typedef struct {
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float A, B, C, alpha, beta, gamma;
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/*@}*/
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#if vmdplugin_ABIVERSION > 10
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double physical_time; /**< physical time point associated with this frame */
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#endif
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#if defined(DESRES_READ_TIMESTEP2)
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/* HACK to support generic trajectory information */
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@ -217,10 +252,29 @@ typedef struct {
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int ysize; /**< number of grid cells along the Y axis */
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int zsize; /**< number of grid cells along the Z axis */
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#if vmdplugin_ABIVERSION > 16
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int has_scalar; /**< flag indicating presence of scalar volume */
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int has_gradient; /**< flag indicating presence of vector volume */
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int has_variance; /**< flag indicating presence of variance map */
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#endif
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int has_color; /**< flag indicating presence of voxel color data */
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} molfile_volumetric_t;
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#if vmdplugin_ABIVERSION > 16
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/**
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* Volumetric dataset read/write structure with both flag/parameter sets
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* and VMD-allocated pointers for fields to be used by the plugin.
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*/
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typedef struct {
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int setidx; /**< volumetric dataset index to load/save */
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float *scalar; /**< scalar density/potential field data */
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float *gradient; /**< gradient vector field */
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float *variance; /**< variance map indicating signal/noise */
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float *rgb3f; /**< RGB floating point color texture map */
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unsigned char *rgb3u; /**< RGB unsigned byte color texture map */
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} molfile_volumetric_readwrite_t;
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#endif
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/**************************************************************
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@ -231,9 +285,6 @@ typedef struct {
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**************************************************************
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**************************************************************/
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#if vmdplugin_ABIVERSION > 9
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/* macros for the convergence status of a QM calculation. */
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#define MOLFILE_QMSTATUS_UNKNOWN -1 /* don't know yet */
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#define MOLFILE_QMSTATUS_OPT_CONV 0 /* optimization converged */
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@ -485,8 +536,6 @@ typedef struct {
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} molfile_qm_timestep_t;
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#endif
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/**************************************************************
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**************************************************************/
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@ -609,12 +658,8 @@ typedef struct {
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* This function can be called only after read_structure().
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* Return MOLFILE_SUCCESS if no errors occur.
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*/
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#if vmdplugin_ABIVERSION > 14
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int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
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int **bondtype, int *nbondtypes, char ***bondtypename);
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#else
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int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder);
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#endif
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/**
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* XXX this function will be augmented and possibly superceded by a
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@ -684,6 +729,9 @@ typedef struct {
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*/
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int (* read_volumetric_data)(void *, int set, float *datablock,
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float *colorblock);
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#if vmdplugin_ABIVERSION > 16
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int (* read_volumetric_data_ex)(void *, molfile_volumetric_readwrite_t *v);
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#endif
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/**
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* Read raw graphics data stored in this file. Return the number of data
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@ -723,14 +771,9 @@ typedef struct {
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* bondtypenames can only be used of bondtypes is also given.
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* Return MOLFILE_SUCCESS if no errors occur.
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*/
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#if vmdplugin_ABIVERSION > 14
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int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
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int *bondtype, int nbondtypes, char **bondtypename);
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#else
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int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
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#endif
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#if vmdplugin_ABIVERSION > 9
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/**
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* Write the specified volumetric data set into the space pointed to by
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* datablock. The * allocated for the datablock must be equal to
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@ -740,8 +783,11 @@ typedef struct {
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*/
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int (* write_volumetric_data)(void *, molfile_volumetric_t *metadata,
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float *datablock, float *colorblock);
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#if vmdplugin_ABIVERSION > 16
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int (* write_volumetric_data_ex)(void *, molfile_volumetric_t *metadata,
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molfile_volumetric_readwrite_t *v);
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#endif
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#if vmdplugin_ABIVERSION > 15
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/**
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* Read in Angles, Dihedrals, Impropers, and Cross Terms and optionally types.
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* (Cross terms pertain to the CHARMM/NAMD CMAP feature)
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@ -764,33 +810,6 @@ typedef struct {
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const int *impropers, const int *impropertypes, int numimpropertypes,
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const char **impropertypenames, int numcterms, const int *cterms,
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int ctermcols, int ctermrows);
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#else
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/**
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* Read in Angles, Dihedrals, Impropers, and Cross Terms
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* Forces are in Kcal/mol
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* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
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* as a 2-D matrix)
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*/
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int (* read_angles)(void *,
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int *numangles, int **angles, double **angleforces,
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int *numdihedrals, int **dihedrals, double **dihedralforces,
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int *numimpropers, int **impropers, double **improperforces,
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int *numcterms, int **cterms,
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int *ctermcols, int *ctermrows, double **ctermforces);
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/**
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* Write out Angles, Dihedrals, Impropers, and Cross Terms
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* Forces are in Kcal/mol
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* (Cross terms pertain to the CHARMM/NAMD CMAP feature, forces are given
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* as a 2-D matrix)
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*/
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int (* write_angles)(void *,
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int numangles, const int *angles, const double *angleforces,
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int numdihedrals, const int *dihedrals, const double *dihedralforces,
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int numimpropers, const int *impropers, const double *improperforces,
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int numcterms, const int *cterms,
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int ctermcols, int ctermrows, const double *ctermforces);
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#endif
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/**
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@ -839,14 +858,9 @@ typedef struct {
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*/
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int (* read_timestep)(void *, int natoms, molfile_timestep_t *,
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molfile_qm_metadata_t *, molfile_qm_timestep_t *);
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#endif
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#if vmdplugin_ABIVERSION > 10
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int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
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#endif
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#if vmdplugin_ABIVERSION > 11
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int (* read_qm_timestep_metadata)(void *, molfile_qm_timestep_metadata_t *);
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#endif
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#if defined(DESRES_READ_TIMESTEP2)
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/**
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double * times );
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#endif
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#if vmdplugin_ABIVERSION > 13
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/**
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* Console output, READ-ONLY function pointer.
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* Function pointer that plugins can use for printing to the host
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@ -883,8 +896,8 @@ typedef struct {
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* application-provided services
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*/
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int (* cons_fputs)(const int, const char*);
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#endif
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} molfile_plugin_t;
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#endif
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