gromacs-dev 4.6.5-1build1 / usr / include / gromacs / statutil.h

/*
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 *
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 * Copyright (c) 2001-2004, The GROMACS development team,
 * check out http://www.gromacs.org for more information.
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 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
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#ifndef _statutil_h
#define _statutil_h

#include <stdio.h>
#include "visibility.h"
#include "typedefs.h"
#include "filenm.h"
#include "readinp.h"
#include "wman.h"
#include "pdbio.h"
#include "oenv.h"
#include "gmxfio.h"


#ifdef __cplusplus
extern "C" {
#endif
#if 0 /* avoid screwing up indentation */
}
#endif


/* The code below is to facilitate controlled begin and end of
   trajectory reading. Corresponding routines in
   src/gmxlib/tcontrol.c
 */
enum {
    TBEGIN, TEND, TDELTA, TNR
};

gmx_bool bTimeSet(int tcontrol);

real rTimeValue(int tcontrol);

void setTimeValue(int tcontrol, real value);

/* End trajectory time control */

/* a dedicated status type contains fp, etc. */
typedef struct t_trxstatus t_trxstatus;

typedef int t_first_x (t_trxstatus **status, const char *fn, real *t, rvec **x,
                       matrix box);

typedef gmx_bool t_next_x (t_trxstatus *status, real *t, int natoms, rvec x[],
                           matrix box);

/* I/O function types */


/* LEGACY FUNCTIONS

   The program names, command lines, etc. are now also set in the output_env
   structure. That is now the preferred location, but the functions here
   are still available as legacy functions. Because they all act on inherently
   global informaion, their existence in a multi-threaded environment is not
   a real problem. */

/* Return the name of the program */
GMX_LIBGMX_EXPORT
const char *command_line(void);
void set_command_line(int argc, char *argv[]);

/* set the program name to the provided string, but note
 * that it must be a real file - we determine the library
 * directory from its location!
 */
GMX_LIBGMX_EXPORT
const char *Program(void);
GMX_LIBGMX_EXPORT
void set_program_name(const char *argvzero);
/* Id. without leading directory */
GMX_LIBGMX_EXPORT
const char *ShortProgram(void);

/************************************************
 *             Trajectory functions
 ************************************************/

GMX_LIBGMX_EXPORT
int prec2ndec(real prec);
/* Convert precision in 1/(nm) to number of decimal places */

GMX_LIBGMX_EXPORT
void clear_trxframe(t_trxframe *fr, gmx_bool bFirst);
/* Set all content gmx_booleans to FALSE.
 * When bFirst = TRUE, set natoms=-1, all pointers to NULL
 *                     and all data to zero.
 */

GMX_LIBGMX_EXPORT
void set_trxframe_ePBC(t_trxframe *fr, int ePBC);
/* Set the type of periodic boundary conditions, ePBC=-1 is not set */

GMX_LIBGMX_EXPORT
int nframes_read(t_trxstatus *status);
/* Returns the number of frames read from the trajectory */

GMX_LIBGMX_EXPORT
int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
                           atom_id *ind, gmx_conect gc);
/* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */

GMX_LIBGMX_EXPORT
int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc);
/* Write a frame to a TRX file.
 * Only entries for which the gmx_boolean is TRUE will be written,
 * except for step, time, lambda and/or box, which may not be
 * omitted for certain trajectory formats.
 * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
 * the precision is set to 1000.
 * gc is important for pdb file writing only and may be NULL.
 */

GMX_LIBGMX_EXPORT
int write_trx(t_trxstatus *status, int nind, atom_id *ind, t_atoms *atoms,
              int step, real time, matrix box, rvec x[], rvec *v,
              gmx_conect gc);
/* Write an indexed frame to a TRX file.
 * v can be NULL.
 * atoms can be NULL for file types which don't need atom names.
 */

GMX_LIBGMX_EXPORT
void close_trx(t_trxstatus *status);
/* Close trj file as opened with read_first_x, read_frist_frame
 * or open_trx. Identical to close_trj.
 */

GMX_LIBGMX_EXPORT
t_trxstatus *open_trx(const char *outfile, const char *filemode);
/* Open a TRX file and return an allocated status pointer */

/* get a fileio from a trxstatus */
GMX_LIBGMX_EXPORT
t_fileio *trx_get_fileio(t_trxstatus *status);


GMX_LIBGMX_EXPORT
gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
/* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
 * larger than the float/double precision.
 */

#ifdef GMX_DOUBLE
#define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
#else
#define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
#endif

int check_times2(real t, real t0, real tp, real tpp, gmx_bool bDouble);
/* This routine checkes if the read-in time is correct or not;
 * returns -1 if t<tbegin or t MOD dt = t0,
 *          0 if tbegin <= t <=tend+margin,
 *          1 if t>tend
 * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
 * tp and tpp should be the time of the previous frame and the one before.
 * The mod is done with single or double precision accuracy depending
 * on the value of bDouble.
 */

GMX_LIBGMX_EXPORT
int check_times(real t);
/* This routine checkes if the read-in time is correct or not;
 * returns -1 if t<tbegin,
 *          0 if tbegin <= t <=tend,
 *          1 if t>tend
 */





/* For trxframe.flags, used in trxframe read routines.
 * When a READ flag is set, the field will be read when present,
 * but a frame might be returned which does not contain the field.
 * When a NEED flag is set, frames not containing the field will be skipped.
 */
#define TRX_READ_X    (1<<0)
#define TRX_NEED_X    (1<<1)
#define TRX_READ_V    (1<<2)
#define TRX_NEED_V    (1<<3)
#define TRX_READ_F    (1<<4)
#define TRX_NEED_F    (1<<5)
/* Useful for reading natoms from a trajectory without skipping */
#define TRX_DONT_SKIP (1<<6)

/* For trxframe.not_ok */
#define HEADER_NOT_OK (1<<0)
#define DATA_NOT_OK   (1<<1)
#define FRAME_NOT_OK  (HEADER_NOT_OK | DATA_NOT_OK)

GMX_LIBGMX_EXPORT
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
                     const char *fn, t_trxframe *fr, int flags);
/* Read the first frame which is in accordance with flags, which are
 * defined further up in this file.
 * Returns natoms when succeeded, 0 otherwise.
 * Memory will be allocated for flagged entries.
 * The flags are copied to fr for subsequent calls to read_next_frame.
 * Returns TRUE when succeeded, FALSE otherwise.
 */

GMX_LIBGMX_EXPORT
gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
                         t_trxframe *fr);
/* Reads the next frame which is in accordance with fr->flags.
 * Returns TRUE when succeeded, FALSE otherwise.
 */

GMX_LIBGMX_EXPORT
int read_first_x(const output_env_t oenv, t_trxstatus **status,
                 const char *fn, real *t, rvec **x, matrix box);
/* These routines read first coordinates and box, and allocates
 * memory for the coordinates, for a trajectory file.
 * The routine returns the number of atoms, or 0 when something is wrong.
 * The integer in status should be passed to calls of read_next_x
 */

GMX_LIBGMX_EXPORT
gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t,
                     int natoms, rvec x[], matrix box);
/* Read coordinates and box from a trajectory file. Return TRUE when all well,
 * or FALSE when end of file (or last frame requested by user).
 * status is the integer set in read_first_x.
 */

GMX_LIBGMX_EXPORT
void close_trj(t_trxstatus *status);
/* Close trj file as opened with read_first_x, read_frist_frame
 * or open_trx. Identical to close_trx.
 */

void rewind_trj(t_trxstatus *status);
/* Rewind trj file as opened with read_first_x */

GMX_LIBGMX_EXPORT
t_topology *read_top(const char *fn, int *ePBC);
/* Extract a topology data structure from a topology file.
 * If ePBC!=NULL *ePBC gives the pbc type.
 */

/*****************************************************
 *         Some command line parsing routines
 *****************************************************/

#define PCA_CAN_VIEW       (1<<5)
/* add option -w to view output files (must be implemented in program) */
#define PCA_CAN_BEGIN      (1<<6)
#define PCA_CAN_END        (1<<7)
#define PCA_CAN_DT         (1<<14)
#define PCA_CAN_TIME       (PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_DT)
/* adds options -b and -e for begin and end time for reading trajectories */
#define PCA_TIME_UNIT      (1<<15)
/* set time unit for output */
#define PCA_KEEP_ARGS      (1<<8)
/* keep parsed args in argv (doesn't make sense without NOEXIT_ON_ARGS) */
#define PCA_SILENT         (1<<9)
/* don't print options by default */
#define PCA_CAN_SET_DEFFNM (1<<10)
/* does something for non-master mdrun nodes */
#define PCA_NOEXIT_ON_ARGS (1<<11)
/* no fatal_error when invalid options are encountered */
#define PCA_QUIET          (1<<12)
/* does something for non-master mdrun nodes */
#define PCA_BE_NICE        (1<<13)
/* Default to low priority, unless configured with --disable-nice */
#define PCA_NOT_READ_NODE  (1<<16)
/* Is this node not reading: for parallel all nodes but the master */

int iscan(int argc, char *argv[], int *i);
/* Scan an int from the argument at *i. If the argument length
 * is > 2, the int is assumed to be in the remainder of the arg,
 * eg: -p32, else the int is assumed to be in the next argument
 * eg: -p 32. If neither is the case the routine exits with an error,
 * otherwise it returns the value found. If the value is in the next
 * argument *i is incremented. You typically would want to pass
 * a loop variable to this routine.
 */
gmx_large_int_t istepscan(int argc, char *argv[], int *i);
/* Same as above, but for large integer values */

double dscan(int argc, char *argv[], int *i);
/* Routine similar to the above, but working on doubles. */

char *sscan(int argc, char *argv[], int *i);
/* Routine similar to the above, but working on strings. The pointer
 * returned is a pointer to the argv field.
 */

void vscan(int argc, char *argv[], int *i, rvec *vec);
/* Routine similar to the above, but working on rvecs. */

GMX_LIBGMX_EXPORT
int nenum(const char *const enumc[]);
/* returns ordinal number of selected enum from args
 * depends on enumc[0] pointing to one of the other elements
 * array must be terminated by a NULL pointer
 */

GMX_LIBGMX_EXPORT
void parse_common_args(int *argc, char *argv[], unsigned long Flags,
                       int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
                       int ndesc, const char **desc,
                       int nbugs, const char **bugs,
                       output_env_t *oenv);
/* Get arguments from the arg-list. The arguments extracted
 * are removed from the list. If manual is NULL a default message is displayed
 * when errors are encountered. The Flags argument, when non-0 enables
 * some input checks. Using this routine also means that the arguments
 * -b and -e will be used for begin and end time, whether this is
 * appropriate or not!
 */

#ifdef __cplusplus
}
#endif

#endif