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38 #ifndef GMX_FILEIO_TRXIO_H
39 #define GMX_FILEIO_TRXIO_H
41 #include "../legacyheaders/typedefs.h"
43 #include "../legacyheaders/readinp.h"
45 #include "../legacyheaders/oenv.h"
51 #if 0 /* avoid screwing up indentation */
55 /* a dedicated status type contains fp, etc. */
56 typedef struct t_trxstatus t_trxstatus;
58 /* I/O function types */
60 /************************************************
61 * Trajectory functions
62 ************************************************/
64 int prec2ndec(real prec);
65 /* Convert precision in 1/(nm) to number of decimal places */
67 void clear_trxframe(t_trxframe *fr, gmx_bool bFirst);
68 /* Set all content gmx_booleans to FALSE.
69 * When bFirst = TRUE, set natoms=-1, all pointers to NULL
70 * and all data to zero.
73 void set_trxframe_ePBC(t_trxframe *fr, int ePBC);
74 /* Set the type of periodic boundary conditions, ePBC=-1 is not set */
76 int nframes_read(t_trxstatus *status);
77 /* Returns the number of frames read from the trajectory */
79 int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
80 const atom_id *ind, gmx_conect gc);
81 /* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
83 int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc);
84 /* Write a frame to a TRX file.
85 * Only entries for which the gmx_boolean is TRUE will be written,
86 * except for step, time, lambda and/or box, which may not be
87 * omitted for certain trajectory formats.
88 * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
89 * the precision is set to 1000.
90 * gc is important for pdb file writing only and may be NULL.
93 int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
94 int step, real time, matrix box, rvec x[], rvec *v,
96 /* Write an indexed frame to a TRX file.
98 * atoms can be NULL for file types which don't need atom names.
101 void close_trx(t_trxstatus *status);
102 /* Close trj file as opened with read_first_x, read_frist_frame
103 * or open_trx. Identical to close_trj.
106 t_trxstatus *open_trx(const char *outfile, const char *filemode);
107 /* Open a TRX file and return an allocated status pointer */
109 /* get a fileio from a trxstatus */
110 t_fileio *trx_get_fileio(t_trxstatus *status);
113 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
114 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
115 * larger than the float/double precision.
119 #define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
121 #define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
124 int check_times2(real t, real t0, gmx_bool bDouble);
125 /* This routine checkes if the read-in time is correct or not;
126 * returns -1 if t<tbegin or t MOD dt = t0,
127 * 0 if tbegin <= t <=tend+margin,
129 * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
130 * tp and tpp should be the time of the previous frame and the one before.
131 * The mod is done with single or double precision accuracy depending
132 * on the value of bDouble.
135 int check_times(real t);
136 /* This routine checkes if the read-in time is correct or not;
137 * returns -1 if t<tbegin,
138 * 0 if tbegin <= t <=tend,
146 /* For trxframe.flags, used in trxframe read routines.
147 * When a READ flag is set, the field will be read when present,
148 * but a frame might be returned which does not contain the field.
149 * When a NEED flag is set, frames not containing the field will be skipped.
151 #define TRX_READ_X (1<<0)
152 #define TRX_NEED_X (1<<1)
153 #define TRX_READ_V (1<<2)
154 #define TRX_NEED_V (1<<3)
155 #define TRX_READ_F (1<<4)
156 #define TRX_NEED_F (1<<5)
157 /* Useful for reading natoms from a trajectory without skipping */
158 #define TRX_DONT_SKIP (1<<6)
160 /* For trxframe.not_ok */
161 #define HEADER_NOT_OK (1<<0)
162 #define DATA_NOT_OK (1<<1)
163 #define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
165 int read_first_frame(const output_env_t oenv, t_trxstatus **status,
166 const char *fn, t_trxframe *fr, int flags);
167 /* Read the first frame which is in accordance with flags, which are
168 * defined further up in this file.
169 * Returns natoms when succeeded, 0 otherwise.
170 * Memory will be allocated for flagged entries.
171 * The flags are copied to fr for subsequent calls to read_next_frame.
172 * Returns TRUE when succeeded, FALSE otherwise.
175 gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
177 /* Reads the next frame which is in accordance with fr->flags.
178 * Returns TRUE when succeeded, FALSE otherwise.
181 int read_first_x(const output_env_t oenv, t_trxstatus **status,
182 const char *fn, real *t, rvec **x, matrix box);
183 /* These routines read first coordinates and box, and allocates
184 * memory for the coordinates, for a trajectory file.
185 * The routine returns the number of atoms, or 0 when something is wrong.
186 * The integer in status should be passed to calls of read_next_x
189 gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t, rvec x[], matrix box);
190 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
191 * or FALSE when end of file (or last frame requested by user).
192 * status is the integer set in read_first_x.
195 void close_trj(t_trxstatus *status);
196 /* Close trj file as opened with read_first_x, read_frist_frame
197 * or open_trx. Identical to close_trx.
200 void rewind_trj(t_trxstatus *status);
201 /* Rewind trj file as opened with read_first_x */
203 t_topology *read_top(const char *fn, int *ePBC);
204 /* Extract a topology data structure from a topology file.
205 * If ePBC!=NULL *ePBC gives the pbc type.