set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_set;
#endif
int xout, vout, fout;
-// int gcd = -1, lowest = -1;
+ int gcd = -1, lowest = -1;
char compression;
tng_set_frames_per_frame_set(tng, bUseLossyCompression, ir);
if (bUseLossyCompression)
{
xout = ir->nstxout_compressed;
- vout = 0;
- fout = 0;
+
+ /* If there is no uncompressed coordinate output write forces
+ and velocities to the compressed tng file. */
+ if (ir->nstxout)
+ {
+ vout = 0;
+ fout = 0;
+ }
+ else
+ {
+ vout = ir->nstvout;
+ fout = ir->nstfout;
+ }
compression = TNG_TNG_COMPRESSION;
}
else
set_writing_interval(tng, xout, 3, TNG_TRAJ_POSITIONS,
"POSITIONS", TNG_PARTICLE_BLOCK_DATA,
compression);
- /* The design of TNG makes it awkward to try to write a box
- * with multiple periodicities, which might be co-prime. Since
- * the use cases for the box with a frame consisting only of
- * velocities seem low, for now we associate box writing with
- * position writing. */
- set_writing_interval(tng, xout, 9, TNG_TRAJ_BOX_SHAPE,
- "BOX SHAPE", TNG_NON_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
/* TODO: if/when we write energies to TNG also, reconsider how
* and when box information is written, because GROMACS
* behaviour pre-5.0 was to write the box with every
* trajectory frame and every energy frame, and probably
* people depend on this. */
- /* TODO: If we need to write lambda values at steps when
- * positions (or other data) are not also being written, then
- * code in mdoutf.c will need to match however that is
- * organized here. */
- set_writing_interval(tng, xout, 1, TNG_GMX_LAMBDA,
- "LAMBDAS", TNG_NON_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
-
- /* FIXME: gcd and lowest currently not used. */
-// gcd = greatest_common_divisor_if_positive(gcd, xout);
-// if (lowest < 0 || xout < lowest)
-// {
-// lowest = xout;
-// }
+ gcd = greatest_common_divisor_if_positive(gcd, xout);
+ if (lowest < 0 || xout < lowest)
+ {
+ lowest = xout;
+ }
}
if (vout)
{
"VELOCITIES", TNG_PARTICLE_BLOCK_DATA,
compression);
- /* FIXME: gcd and lowest currently not used. */
-// gcd = greatest_common_divisor_if_positive(gcd, vout);
-// if (lowest < 0 || vout < lowest)
-// {
-// lowest = vout;
-// }
+ gcd = greatest_common_divisor_if_positive(gcd, vout);
+ if (lowest < 0 || vout < lowest)
+ {
+ lowest = vout;
+ }
}
if (fout)
{
"FORCES", TNG_PARTICLE_BLOCK_DATA,
TNG_GZIP_COMPRESSION);
- /* FIXME: gcd and lowest currently not used. */
-// gcd = greatest_common_divisor_if_positive(gcd, fout);
-// if (lowest < 0 || fout < lowest)
-// {
-// lowest = fout;
-// }
- }
- /* FIXME: See above. gcd interval for lambdas is disabled. */
-// if (gcd > 0)
-// {
-// /* Lambdas written at an interval of the lowest common denominator
-// * of other output */
-// set_writing_interval(tng, gcd, 1, TNG_GMX_LAMBDA,
-// "LAMBDAS", TNG_NON_PARTICLE_BLOCK_DATA,
-// TNG_GZIP_COMPRESSION);
-//
-// if (gcd < lowest / 10)
-// {
-// gmx_warning("The lowest common denominator of trajectory output is "
-// "every %d step(s), whereas the shortest output interval "
-// "is every %d steps.", gcd, lowest);
-// }
-// }
+ gcd = greatest_common_divisor_if_positive(gcd, fout);
+ if (lowest < 0 || fout < lowest)
+ {
+ lowest = fout;
+ }
+ }
+ if (gcd > 0)
+ {
+ /* Lambdas and box shape written at an interval of the lowest common
+ denominator of other output */
+ set_writing_interval(tng, gcd, 1, TNG_GMX_LAMBDA,
+ "LAMBDAS", TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
+
+ set_writing_interval(tng, gcd, 9, TNG_TRAJ_BOX_SHAPE,
+ "BOX SHAPE", TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
+ if (gcd < lowest / 10)
+ {
+ gmx_warning("The lowest common denominator of trajectory output is "
+ "every %d step(s), whereas the shortest output interval "
+ "is every %d steps.", gcd, lowest);
+ }
+ }
}
#endif
{
gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
}
- /* TNG-MF1 compression only compresses positions and velocities. Use lossless
- * compression for box shape regardless of output mode */
- if (write_data(tng, step, elapsedSeconds,
- reinterpret_cast<const real *>(box),
- 9, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE",
- TNG_NON_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION) != TNG_SUCCESS)
- {
- gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
- }
}
if (v)
}
/* TNG-MF1 compression only compresses positions and velocities. Use lossless
- * compression for lambdas regardless of output mode */
+ * compression for lambdas and box shape regardless of output mode */
+ if (write_data(tng, step, elapsedSeconds,
+ reinterpret_cast<const real *>(box),
+ 9, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE",
+ TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION) != TNG_SUCCESS)
+ {
+ gmx_file("Cannot write TNG trajectory frame; maybe you are out of disk space?");
+ }
+
if (write_data(tng, step, elapsedSeconds,
reinterpret_cast<const real *>(&lambda),
1, TNG_GMX_LAMBDA, "LAMBDAS",
sprintf(filemode, bAppendFiles ? "a+" : "w+");
+ if (EI_DYNAMICS(ir->eI) &&
+ ir->nstxout_compressed > 0)
+ {
+ const char *filename;
+ filename = ftp2fn(efCOMPRESSED, nfile, fnm);
+ switch (fn2ftp(filename))
+ {
+ case efXTC:
+ of->fp_xtc = open_xtc(filename, filemode);
+ break;
+ case efTNG:
+ gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
+ if (filemode[0] == 'w')
+ {
+ gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
+ }
+ bCiteTng = TRUE;
+ break;
+ default:
+ gmx_incons("Invalid reduced precision file format");
+ }
+ }
if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
#ifndef GMX_FAHCORE
&&
{
case efTRR:
case efTRN:
- of->fp_trn = gmx_trr_open(filename, filemode);
+ /* If there is no uncompressed coordinate output and
+ there is compressed TNG output write forces
+ and/or velocities to the TNG file instead. */
+ if (ir->nstxout != 0 || ir->nstxout_compressed == 0 ||
+ !of->tng_low_prec)
+ {
+ of->fp_trn = gmx_trr_open(filename, filemode);
+ }
break;
case efTNG:
gmx_tng_open(filename, filemode[0], &of->tng);
gmx_incons("Invalid full precision file format");
}
}
- if (EI_DYNAMICS(ir->eI) &&
- ir->nstxout_compressed > 0)
- {
- const char *filename;
- filename = ftp2fn(efCOMPRESSED, nfile, fnm);
- switch (fn2ftp(filename))
- {
- case efXTC:
- of->fp_xtc = open_xtc(filename, filemode);
- break;
- case efTNG:
- gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
- if (filemode[0] == 'w')
- {
- gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
- }
- bCiteTng = TRUE;
- break;
- default:
- gmx_incons("Invalid reduced precision file format");
- }
- }
if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
{
of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
}
}
- gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box,
- top_global->natoms,
- (mdof_flags & MDOF_X) ? state_global->x : NULL,
- (mdof_flags & MDOF_V) ? global_v : NULL,
- (mdof_flags & MDOF_F) ? f_global : NULL);
+ /* If a TNG file is open for uncompressed coordinate output also write
+ velocities and forces to it. */
+ else if (of->tng)
+ {
+ gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
+ state_local->box,
+ top_global->natoms,
+ (mdof_flags & MDOF_X) ? state_global->x : NULL,
+ (mdof_flags & MDOF_V) ? global_v : NULL,
+ (mdof_flags & MDOF_F) ? f_global : NULL);
+ }
+ /* If only a TNG file is open for compressed coordinate output (no uncompressed
+ coordinate output) also write forces and velocities to it. */
+ else if (of->tng_low_prec)
+ {
+ gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
+ state_local->box,
+ top_global->natoms,
+ (mdof_flags & MDOF_X) ? state_global->x : NULL,
+ (mdof_flags & MDOF_V) ? global_v : NULL,
+ (mdof_flags & MDOF_F) ? f_global : NULL);
+ }
}
if (mdof_flags & MDOF_X_COMPRESSED)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff