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update molfile plugin headers with latest versions from VMD

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This commit is contained in:
Axel Kohlmeyer
2020-09-12 14:04:23 -04:00
parent 1597cd5dcb
commit bc850bcd97
2 changed files with 109 additions and 22 deletions
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127
lib/molfile/molfile_plugin.h
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@ -11,7 +11,7 @@
*
* $RCSfile: molfile_plugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.108 $ $Date: 2016/02/26 03:17:01 $
* $Revision: 1.112 $ $Date: 2019/10/17 06:12:24 $
*
***************************************************************************/
@ -111,7 +111,7 @@ 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
#if 0 && vmdplugin_ABIVERSION > 10000
/* 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 */
@ -187,13 +187,58 @@ typedef struct molfile_timestep_metadata {
int has_velocities; /**< if timesteps have velocities */
} molfile_timestep_metadata_t;
/*
* Per-timestep atom coordinates and periodic cell information
*
* Per-timestep atom coordinates, velocities, forces, energies,
* and periodic cell information
*
*/
#if 0
/**
* Periodically stored energies of various kinds
*/
typedef struct {
int energyflags; // XXX indicate use and semantics of data fields
double total_energy; // XXX these copied from DESRES_READ_TIMESTEP2 case
double potential_energy;
double kinetic_energy;
double extended_energy;
double force_energy;
double total_pressure;
// Alchemical free energy methods need to store individual energy samples.
// We don't really want pre-averaged quantities, they lead to problems later.
double lambda; // data gen sim parm: + aux scheduling + soft core parm
double temperature; // temp set by thermostat
// either we use deltaU, or we store U and Uprime...
double deltaU; // Ulambda - Ulambdaprime
double Ulambda; // U for lambda
double Ulambdaprime; // U for lambdaprime
// IDWS methods
// XXX both values of lambdaprime and required de-interleaving information
// Replica exchange methods
// XXX rectangle sample params?
// REST2 method
// XXX
} molfile_energies_t;
#endif
/**
* Per-timestep atom coordinates, velocities, time, energies
* and periodic cell info
*/
typedef struct {
float *coords; /**< coordinates of all atoms, arranged xyzxyzxyz */
float *velocities; /**< space for velocities of all atoms; same layout */
/**< nullptr unless has_velocities is set */
/**< NULL unless has_velocities is set */
/*@{*/
/**
@ -517,7 +562,7 @@ typedef struct {
* form {orbital1(c1),orbital1(c2),.....,orbitalM(cN)} */
float *orbital_energies; /**< list of orbital energies for wavefunction */
float *occupancies; /**< orbital occupancies */
int *orbital_ids; /**< orbital ID numbers; If nullptr then VMD will
int *orbital_ids; /**< orbital ID numbers; If NULL then VMD will
* assume 1,2,3,...num_orbs. */
} molfile_qm_wavefunction_t;
@ -588,7 +633,7 @@ color r, g, b
/**
* Main file reader API. Any function in this struct may be nullptr
* 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.
*/
@ -599,7 +644,7 @@ typedef struct {
vmdplugin_HEAD
/**
* Filename extension for this file type. May be nullptr 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"
@ -611,7 +656,7 @@ typedef struct {
const char *filename_extension;
/**
* Try to open the file for reading. Return an opaque handle, or nullptr on
* 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.
* Filetype should be the name under which this plugin was registered;
@ -638,20 +683,20 @@ typedef struct {
* the caller.
* 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 nullptr to indicate that no bond
* 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.
*
* 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 nullptr, 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
* will contain the bond type index for each from/to pair. These numbers
* are consecutive integers starting from 0.
* the bondtypenames list, contains the corresponding names, if available,
* as a nullptr string terminated list. nbondtypes is provided for convenience
* as a NULL string terminated list. nbondtypes is provided for convenience
* and consistency checking.
*
* These arrays must be freed by the plugin in the close_file_read function.
@ -662,11 +707,11 @@ typedef struct {
int **bondtype, int *nbondtypes, char ***bondtypename);
/**
* XXX this function will be augmented and possibly superseded 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 nullptr, then
* 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.
@ -684,7 +729,7 @@ typedef struct {
/**
* Open a coordinate file for writing using the given header information.
* Return an opaque handle, or nullptr on failure. The application must
* Return an opaque handle, or NULL on failure. The application must
* specify the number of atoms to be written.
* filetype should be the name under which this plugin was registered.
*/
@ -757,7 +802,7 @@ typedef struct {
* from/to and to/from versions of each.
* This function must be called before write_structure().
*
* Like the read_bonds() routine, the bondorder pointer is set to nullptr
* Like the read_bonds() routine, the bondorder pointer is set to NULL
* 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.
@ -767,7 +812,7 @@ typedef struct {
* index (consecutive integers starting from 0) and bondtypenames
* contain the corresponding strings, in case the naming/numbering
* scheme is different from the index numbers.
* if the pointers are set to nullptr, then this information is not available.
* 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.
*/
@ -839,16 +884,39 @@ typedef struct {
int (* read_qm_rundata)(void *, molfile_qm_t *qmdata);
/**
* Query the molfile plugin to determine whether or not memory
* allocations used for atomic coordinates and PBC unit cell information
* need to be aligned to a particular virtual memory or filesystem
* page size boundary to facilitate kernel-bypass unbuffered I/O,
* e.g., as used by jsplugin. This API should be called prior to the
* first call to read a timestep. The required page alignment size
* (in bytes) is returned to the caller. If this API has not been
* called, then the molfile plugin should revert to standard
* kernel-buffered I/O and suffer the associated performance loss.
* The caller can be assured that the plugin will not request any
* page alignment size that is greater than the value of
* MOLFILE_DIRECTIO_MAX_BLOCK_SIZE, both as a runtime sanity check,
* and to ensure that a caller that is unable to perform the max
* aligned allocation doesn't call the API in the first place.
* If a page-aligned allocation is not required for the file being read,
* the plugin will return an alignment size of 1.
*/
#if vmdplugin_ABIVERSION > 17
int (* read_timestep_pagealign_size)(void *, int *pagealignsize);
#endif
/**
* 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 nullptr, then the coordinate or qm data should be skipped.
* 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
* data from a QM run, the application may provide any combination of
* valid, or nullptr 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
@ -862,6 +930,25 @@ typedef struct {
int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
int (* read_qm_timestep_metadata)(void *, molfile_qm_timestep_metadata_t *);
#if defined(EXPERIMENTAL_DIRECTIO_APIS)
/**
* Calculate file offsets and I/O lengths for performing
* kernel-bypass direct I/O or using GPU-Direct Storage APIs,
* thereby enabling peak I/O rates to be achieved for analysis
* worksloads like clustering of trajectories.
*/
int (* calc_fileoffsets_timestep)(void *,
molfile_ssize_t frameindex,
int firstatom,
int lastatom,
int *firstatom,
int *pageoffset,
molfile_ssize_t *startoffset,
molfile_ssize_t *readlen);
#endif
#if defined(DESRES_READ_TIMESTEP2)
/**
* Read a specified timestep!
@ -886,9 +973,9 @@ typedef struct {
* caller the ability to prioritize, buffer, and redirect console messages
* to an appropriate output channel, window, etc. This enables the use of
* graphical consoles like TkCon without losing console output from plugins.
* If the function pointer is nullptr, no console output service is provided
* If the function pointer is NULL, no console output service is provided
* by the calling application, and the output should default to stdout
* stream. If the function pointer is non-nullptr, all output will be
* stream. If the function pointer is non-NULL, all output will be
* subsequently dealt with by the calling application.
*
* XXX this should really be put into a separate block of

4
lib/molfile/vmdplugin.h
View File

@ -11,7 +11,7 @@
*
* $RCSfile: vmdplugin.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
* $Revision: 1.33 $ $Date: 2015/10/29 05:10:54 $
* $Revision: 1.34 $ $Date: 2018/05/02 03:12:56 $
*
***************************************************************************/
@ -144,7 +144,7 @@ typedef struct {
/**
* Use this macro to initialize the abiversion member of each plugin
*/
#define vmdplugin_ABIVERSION 17
#define vmdplugin_ABIVERSION 18
/*@{*/
/** Use this macro to indicate a plugin's thread-safety at registration time */