#include "tngio.h"
#include "trajectory_writing.h"
#include "checkpoint.h"
+#include "copyrite.h"
struct gmx_mdoutf {
t_fileio *fp_trn;
};
-gmx_mdoutf_t init_mdoutf(int nfile, const t_filenm fnm[], int mdrun_flags,
- const t_commrec *cr, const t_inputrec *ir,
- gmx_mtop_t *top_global,
+gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
+ int mdrun_flags, const t_commrec *cr,
+ const t_inputrec *ir, gmx_mtop_t *top_global,
const output_env_t oenv)
{
gmx_mdoutf_t of;
char filemode[3];
- gmx_bool bAppendFiles;
+ gmx_bool bAppendFiles, bCiteTng = FALSE;
int i;
snew(of, 1);
{
gmx_tng_prepare_md_writing(of->tng, top_global, ir);
}
+ bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid full precision file format");
{
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 (bCiteTng)
+ {
+ please_cite(fplog, "Lundborg2014");
+ }
+
return of;
}
* Returns a pointer to a data structure with all output file pointers
* and names required by mdrun.
*/
-gmx_mdoutf_t init_mdoutf(int nfile,
+gmx_mdoutf_t init_mdoutf(FILE *fplog,
+ int nfile,
const t_filenm fnm[],
int mdrun_flags,
const t_commrec *cr,
"C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae",
"Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail",
"Biophys. J.",
- 101, 2011, "809-817"}
+ 101, 2011, "809-817"},
+ { "Lundborg2014",
+ "M. Lundborg, R. Apostolov, D. Spangberg, A. Gardenas, D. van der Spoel and E. Lindahl",
+ "An efficient and extensible format, library, and API for binary trajectory data from molecular simulations",
+ "J. Comput. Chem.",
+ 35, 2014, "260-269"}
};
#define NSTR (int)asize(citedb)
*gstat = global_stat_init(ir);
}
- *outf = init_mdoutf(nfile, fnm, 0, cr, ir, top_global, NULL);
+ *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL);
snew(*enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
if (nfile != -1)
{
- *outf = init_mdoutf(nfile, fnm, Flags, cr, ir, mtop, oenv);
+ *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv);
*mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : mdoutf_get_fp_ene(*outf),
mtop, ir, mdoutf_get_fp_dhdl(*outf));