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38 #ifndef GMX_FILEIO_TRXIO_H
39 #define GMX_FILEIO_TRXIO_H
41 #include "gromacs/fileio/filenm.h"
42 #include "gromacs/fileio/gmxfio.h"
43 #include "gromacs/fileio/pdbio.h"
44 #include "gromacs/legacyheaders/oenv.h"
45 #include "gromacs/legacyheaders/readinp.h"
50 #if 0 /* avoid screwing up indentation */
59 /* a dedicated status type contains fp, etc. */
60 typedef struct t_trxstatus t_trxstatus;
62 /* I/O function types */
64 /************************************************
65 * Trajectory functions
66 ************************************************/
68 int prec2ndec(real prec);
69 /* Convert precision in 1/(nm) to number of decimal places */
71 /*! \brief Convert number of decimal places to trajectory precision in
73 real ndec2prec(int ndec);
75 void clear_trxframe(struct t_trxframe *fr, gmx_bool bFirst);
76 /* Set all content gmx_booleans to FALSE.
77 * When bFirst = TRUE, set natoms=-1, all pointers to NULL
78 * and all data to zero.
81 void set_trxframe_ePBC(struct t_trxframe *fr, int ePBC);
82 /* Set the type of periodic boundary conditions, ePBC=-1 is not set */
84 int nframes_read(t_trxstatus *status);
85 /* Returns the number of frames read from the trajectory */
87 int write_trxframe_indexed(t_trxstatus *status, struct t_trxframe *fr, int nind,
88 const atom_id *ind, gmx_conect gc);
89 /* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
91 int write_trxframe(t_trxstatus *status, struct t_trxframe *fr, gmx_conect gc);
92 /* Write a frame to a TRX file.
93 * Only entries for which the gmx_boolean is TRUE will be written,
94 * except for step, time, lambda and/or box, which may not be
95 * omitted for certain trajectory formats.
96 * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
97 * the precision is set to 1000.
98 * gc is important for pdb file writing only and may be NULL.
101 int write_trx(t_trxstatus *status, int nind, const atom_id *ind, struct t_atoms *atoms,
102 int step, real time, matrix box, rvec x[], rvec *v,
104 /* Write an indexed frame to a TRX file.
106 * atoms can be NULL for file types which don't need atom names.
109 void trjtools_gmx_prepare_tng_writing(const char *filename,
115 const struct gmx_mtop_t *mtop,
116 const atom_id *index,
117 const char *index_group_name);
118 /* Sets up *out for writing TNG. If *in != NULL and contains a TNG trajectory
119 * some data, e.g. molecule system, will be copied over from *in to *out.
120 * If *in == NULL a file name (infile) of a TNG file can be provided instead
121 * and used for copying data to *out.
122 * If there is no TNG input natoms is used to create "implicit atoms" (no atom
123 * or molecular data present). If natoms == -1 the number of atoms are
124 * not known (or there is already a TNG molecule system to copy, in which case
125 * natoms is not required anyhow). If an group of indexed atoms are written
126 * natoms must be the length of index. index_group_name is the name of the
130 /*! \brief Write a trxframe to the TNG file in status.
132 * This function is needed because both t_trxstatus and
133 * tng_trajectory_t are encapsulated, so client trajectory-writing
134 * code with a t_trxstatus can't just call the TNG writing
136 void write_tng_frame(t_trxstatus *status,
137 struct t_trxframe *fr);
139 void close_trx(t_trxstatus *status);
140 /* Close trajectory file as opened with read_first_x, read_frist_frame
141 * or open_trx. Identical to close_trj.
144 t_trxstatus *open_trx(const char *outfile, const char *filemode);
145 /* Open a TRX file and return an allocated status pointer */
147 t_fileio *trx_get_fileio(t_trxstatus *status);
148 /* get a fileio from a trxstatus */
150 float trx_get_time_of_final_frame(t_trxstatus *status);
151 /* get time of final frame. Only supported for TNG and XTC */
153 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
154 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
155 * larger than the float/double precision.
159 #define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
161 #define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
164 int check_times2(real t, real t0, gmx_bool bDouble);
165 /* This routine checkes if the read-in time is correct or not;
166 * returns -1 if t<tbegin or t MOD dt = t0,
167 * 0 if tbegin <= t <=tend+margin,
169 * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
170 * tp and tpp should be the time of the previous frame and the one before.
171 * The mod is done with single or double precision accuracy depending
172 * on the value of bDouble.
175 int check_times(real t);
176 /* This routine checkes if the read-in time is correct or not;
177 * returns -1 if t<tbegin,
178 * 0 if tbegin <= t <=tend,
186 /* For trxframe.flags, used in trxframe read routines.
187 * When a READ flag is set, the field will be read when present,
188 * but a frame might be returned which does not contain the field.
189 * When a NEED flag is set, frames not containing the field will be skipped.
191 #define TRX_READ_X (1<<0)
192 #define TRX_NEED_X (1<<1)
193 #define TRX_READ_V (1<<2)
194 #define TRX_NEED_V (1<<3)
195 #define TRX_READ_F (1<<4)
196 #define TRX_NEED_F (1<<5)
197 /* Useful for reading natoms from a trajectory without skipping */
198 #define TRX_DONT_SKIP (1<<6)
200 /* For trxframe.not_ok */
201 #define HEADER_NOT_OK (1<<0)
202 #define DATA_NOT_OK (1<<1)
203 #define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
205 int read_first_frame(const output_env_t oenv, t_trxstatus **status,
206 const char *fn, struct t_trxframe *fr, int flags);
207 /* Read the first frame which is in accordance with flags, which are
208 * defined further up in this file.
209 * Returns natoms when succeeded, 0 otherwise.
210 * Memory will be allocated for flagged entries.
211 * The flags are copied to fr for subsequent calls to read_next_frame.
212 * Returns TRUE when succeeded, FALSE otherwise.
215 gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
216 struct t_trxframe *fr);
217 /* Reads the next frame which is in accordance with fr->flags.
218 * Returns TRUE when succeeded, FALSE otherwise.
221 int read_first_x(const output_env_t oenv, t_trxstatus **status,
222 const char *fn, real *t, rvec **x, matrix box);
223 /* These routines read first coordinates and box, and allocates
224 * memory for the coordinates, for a trajectory file.
225 * The routine returns the number of atoms, or 0 when something is wrong.
226 * The integer in status should be passed to calls of read_next_x
229 gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t, rvec x[], matrix box);
230 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
231 * or FALSE when end of file (or last frame requested by user).
232 * status is the integer set in read_first_x.
235 void close_trj(t_trxstatus *status);
236 /* Close trajectory file as opened with read_first_x, read_first_frame
237 * or open_trx. Identical to close_trx.
240 void rewind_trj(t_trxstatus *status);
241 /* Rewind trajectory file as opened with read_first_x */
243 struct t_topology *read_top(const char *fn, int *ePBC);
244 /* Extract a topology data structure from a topology file.
245 * If ePBC!=NULL *ePBC gives the pbc type.