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38 #ifndef GMX_FILEIO_TRXIO_H
39 #define GMX_FILEIO_TRXIO_H
41 #include "../legacyheaders/types/topology.h"
42 #include "../legacyheaders/readinp.h"
43 #include "../legacyheaders/oenv.h"
52 #if 0 /* avoid screwing up indentation */
56 /* a dedicated status type contains fp, etc. */
57 typedef struct t_trxstatus t_trxstatus;
59 /* I/O function types */
61 /************************************************
62 * Trajectory functions
63 ************************************************/
65 int prec2ndec(real prec);
66 /* Convert precision in 1/(nm) to number of decimal places */
68 /*! \brief Convert number of decimal places to trajectory precision in
70 real ndec2prec(int ndec);
72 void clear_trxframe(t_trxframe *fr, gmx_bool bFirst);
73 /* Set all content gmx_booleans to FALSE.
74 * When bFirst = TRUE, set natoms=-1, all pointers to NULL
75 * and all data to zero.
78 void set_trxframe_ePBC(t_trxframe *fr, int ePBC);
79 /* Set the type of periodic boundary conditions, ePBC=-1 is not set */
81 int nframes_read(t_trxstatus *status);
82 /* Returns the number of frames read from the trajectory */
84 int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
85 const atom_id *ind, gmx_conect gc);
86 /* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
88 int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc);
89 /* Write a frame to a TRX file.
90 * Only entries for which the gmx_boolean is TRUE will be written,
91 * except for step, time, lambda and/or box, which may not be
92 * omitted for certain trajectory formats.
93 * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
94 * the precision is set to 1000.
95 * gc is important for pdb file writing only and may be NULL.
98 int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
99 int step, real time, matrix box, rvec x[], rvec *v,
101 /* Write an indexed frame to a TRX file.
103 * atoms can be NULL for file types which don't need atom names.
106 void trjtools_gmx_prepare_tng_writing(const char *filename,
112 const gmx_mtop_t *mtop,
113 const atom_id *index,
114 const char *index_group_name);
115 /* Sets up *out for writing TNG. If *in != NULL and contains a TNG trajectory
116 * some data, e.g. molecule system, will be copied over from *in to *out.
117 * If *in == NULL a file name (infile) of a TNG file can be provided instead
118 * and used for copying data to *out.
119 * If there is no TNG input natoms is used to create "implicit atoms" (no atom
120 * or molecular data present). If natoms == -1 the number of atoms are
121 * not known (or there is already a TNG molecule system to copy, in which case
122 * natoms is not required anyhow). If an group of indexed atoms are written
123 * natoms must be the length of index. index_group_name is the name of the
127 /*! \brief Write a trxframe to the TNG file in status.
129 * This function is needed because both t_trxstatus and
130 * tng_trajectory_t are encapsulated, so client trajectory-writing
131 * code with a t_trxstatus can't just call the TNG writing
133 void write_tng_frame(t_trxstatus *status,
136 void close_trx(t_trxstatus *status);
137 /* Close trj file as opened with read_first_x, read_frist_frame
138 * or open_trx. Identical to close_trj.
141 t_trxstatus *open_trx(const char *outfile, const char *filemode);
142 /* Open a TRX file and return an allocated status pointer */
144 t_fileio *trx_get_fileio(t_trxstatus *status);
145 /* get a fileio from a trxstatus */
147 float trx_get_time_of_final_frame(t_trxstatus *status);
148 /* get time of final frame. Only supported for TNG and XTC */
150 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
151 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
152 * larger than the float/double precision.
156 #define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
158 #define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
161 int check_times2(real t, real t0, gmx_bool bDouble);
162 /* This routine checkes if the read-in time is correct or not;
163 * returns -1 if t<tbegin or t MOD dt = t0,
164 * 0 if tbegin <= t <=tend+margin,
166 * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
167 * tp and tpp should be the time of the previous frame and the one before.
168 * The mod is done with single or double precision accuracy depending
169 * on the value of bDouble.
172 int check_times(real t);
173 /* This routine checkes if the read-in time is correct or not;
174 * returns -1 if t<tbegin,
175 * 0 if tbegin <= t <=tend,
183 /* For trxframe.flags, used in trxframe read routines.
184 * When a READ flag is set, the field will be read when present,
185 * but a frame might be returned which does not contain the field.
186 * When a NEED flag is set, frames not containing the field will be skipped.
188 #define TRX_READ_X (1<<0)
189 #define TRX_NEED_X (1<<1)
190 #define TRX_READ_V (1<<2)
191 #define TRX_NEED_V (1<<3)
192 #define TRX_READ_F (1<<4)
193 #define TRX_NEED_F (1<<5)
194 /* Useful for reading natoms from a trajectory without skipping */
195 #define TRX_DONT_SKIP (1<<6)
197 /* For trxframe.not_ok */
198 #define HEADER_NOT_OK (1<<0)
199 #define DATA_NOT_OK (1<<1)
200 #define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
202 int read_first_frame(const output_env_t oenv, t_trxstatus **status,
203 const char *fn, t_trxframe *fr, int flags);
204 /* Read the first frame which is in accordance with flags, which are
205 * defined further up in this file.
206 * Returns natoms when succeeded, 0 otherwise.
207 * Memory will be allocated for flagged entries.
208 * The flags are copied to fr for subsequent calls to read_next_frame.
209 * Returns TRUE when succeeded, FALSE otherwise.
212 gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
214 /* Reads the next frame which is in accordance with fr->flags.
215 * Returns TRUE when succeeded, FALSE otherwise.
218 int read_first_x(const output_env_t oenv, t_trxstatus **status,
219 const char *fn, real *t, rvec **x, matrix box);
220 /* These routines read first coordinates and box, and allocates
221 * memory for the coordinates, for a trajectory file.
222 * The routine returns the number of atoms, or 0 when something is wrong.
223 * The integer in status should be passed to calls of read_next_x
226 gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t, rvec x[], matrix box);
227 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
228 * or FALSE when end of file (or last frame requested by user).
229 * status is the integer set in read_first_x.
232 void close_trj(t_trxstatus *status);
233 /* Close trj file as opened with read_first_x, read_frist_frame
234 * or open_trx. Identical to close_trx.
237 void rewind_trj(t_trxstatus *status);
238 /* Rewind trj file as opened with read_first_x */
240 t_topology *read_top(const char *fn, int *ePBC);
241 /* Extract a topology data structure from a topology file.
242 * If ePBC!=NULL *ePBC gives the pbc type.