#include "force.h"
#include "vcm.h"
#include "smalloc.h"
-#include "futil.h"
+#include "gromacs/fileio/futil.h"
#include "network.h"
#include "rbin.h"
#include "tgroup.h"
-#include "xtcio.h"
-#include "gmxfio.h"
-#include "trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
#include "statutil.h"
#include "domdec.h"
#include "partdec.h"
}
}
-static void moveit(t_commrec *cr, rvec xx[])
-{
- if (!xx)
- {
- return;
- }
-
- move_rvecs(cr, FALSE, FALSE, xx, NULL, (cr->nnodes-cr->npmenodes)-1, NULL);
-}
-
-gmx_mdoutf_t *init_mdoutf(int nfile, const t_filenm fnm[], int mdrun_flags,
- const t_commrec *cr, const t_inputrec *ir,
- const output_env_t oenv)
-{
- gmx_mdoutf_t *of;
- char filemode[3];
- gmx_bool bAppendFiles;
-
- snew(of, 1);
-
- of->fp_trn = NULL;
- of->fp_ene = NULL;
- of->fp_xtc = NULL;
- of->fp_dhdl = NULL;
- of->fp_field = NULL;
-
- of->eIntegrator = ir->eI;
- of->bExpanded = ir->bExpanded;
- of->elamstats = ir->expandedvals->elamstats;
- of->simulation_part = ir->simulation_part;
-
- if (MASTER(cr))
- {
- bAppendFiles = (mdrun_flags & MD_APPENDFILES);
-
- of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
-
- sprintf(filemode, bAppendFiles ? "a+" : "w+");
-
- if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
-#ifndef GMX_FAHCORE
- &&
- !(EI_DYNAMICS(ir->eI) &&
- ir->nstxout == 0 &&
- ir->nstvout == 0 &&
- ir->nstfout == 0)
-#endif
- )
- {
- of->fp_trn = open_trn(ftp2fn(efTRN, nfile, fnm), filemode);
- }
- if (EI_DYNAMICS(ir->eI) &&
- ir->nstxtcout > 0)
- {
- of->fp_xtc = open_xtc(ftp2fn(efXTC, nfile, fnm), filemode);
- of->xtc_prec = ir->xtcprec;
- }
- if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
- {
- of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
- }
- of->fn_cpt = opt2fn("-cpo", nfile, fnm);
-
- if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
- (ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
- EI_DYNAMICS(ir->eI))
- {
- if (bAppendFiles)
- {
- of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl", nfile, fnm), filemode);
- }
- else
- {
- of->fp_dhdl = open_dhdl(opt2fn("-dhdl", nfile, fnm), ir, oenv);
- }
- }
-
- if (opt2bSet("-field", nfile, fnm) &&
- (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
- {
- if (bAppendFiles)
- {
- of->fp_dhdl = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
- filemode);
- }
- else
- {
- of->fp_field = xvgropen(opt2fn("-field", nfile, fnm),
- "Applied electric field", "Time (ps)",
- "E (V/nm)", oenv);
- }
- }
- }
-
- return of;
-}
-
-void done_mdoutf(gmx_mdoutf_t *of)
-{
- if (of->fp_ene != NULL)
- {
- close_enx(of->fp_ene);
- }
- if (of->fp_xtc)
- {
- close_xtc(of->fp_xtc);
- }
- if (of->fp_trn)
- {
- close_trn(of->fp_trn);
- }
- if (of->fp_dhdl != NULL)
- {
- gmx_fio_fclose(of->fp_dhdl);
- }
- if (of->fp_field != NULL)
- {
- gmx_fio_fclose(of->fp_field);
- }
-
- sfree(of);
-}
-
-void write_traj(FILE *fplog, t_commrec *cr,
- gmx_mdoutf_t *of,
- int mdof_flags,
- gmx_mtop_t *top_global,
- gmx_large_int_t step, double t,
- t_state *state_local, t_state *state_global,
- rvec *f_local, rvec *f_global,
- int *n_xtc, rvec **x_xtc)
-{
- int i, j;
- gmx_groups_t *groups;
- rvec *xxtc;
- rvec *local_v;
- rvec *global_v;
-
-#define MX(xvf) moveit(cr, xvf)
-
- /* MRS -- defining these variables is to manage the difference
- * between half step and full step velocities, but there must be a better way . . . */
-
- local_v = state_local->v;
- global_v = state_global->v;
-
- if (DOMAINDECOMP(cr))
- {
- if (mdof_flags & MDOF_CPT)
- {
- dd_collect_state(cr->dd, state_local, state_global);
- }
- else
- {
- if (mdof_flags & (MDOF_X | MDOF_XTC))
- {
- dd_collect_vec(cr->dd, state_local, state_local->x,
- state_global->x);
- }
- if (mdof_flags & MDOF_V)
- {
- dd_collect_vec(cr->dd, state_local, local_v,
- global_v);
- }
- }
- if (mdof_flags & MDOF_F)
- {
- dd_collect_vec(cr->dd, state_local, f_local, f_global);
- }
- }
- else
- {
- if (mdof_flags & MDOF_CPT)
- {
- /* All pointers in state_local are equal to state_global,
- * but we need to copy the non-pointer entries.
- */
- state_global->lambda = state_local->lambda;
- state_global->veta = state_local->veta;
- state_global->vol0 = state_local->vol0;
- copy_mat(state_local->box, state_global->box);
- copy_mat(state_local->boxv, state_global->boxv);
- copy_mat(state_local->svir_prev, state_global->svir_prev);
- copy_mat(state_local->fvir_prev, state_global->fvir_prev);
- copy_mat(state_local->pres_prev, state_global->pres_prev);
- }
- if (cr->nnodes > 1)
- {
- /* Particle decomposition, collect the data on the master node */
- if (mdof_flags & MDOF_CPT)
- {
- if (state_local->flags & (1<<estX))
- {
- MX(state_global->x);
- }
- if (state_local->flags & (1<<estV))
- {
- MX(state_global->v);
- }
- if (state_local->flags & (1<<estSDX))
- {
- MX(state_global->sd_X);
- }
- if (state_global->nrngi > 1)
- {
- if (state_local->flags & (1<<estLD_RNG))
- {
-#ifdef GMX_MPI
- MPI_Gather(state_local->ld_rng,
- state_local->nrng*sizeof(state_local->ld_rng[0]), MPI_BYTE,
- state_global->ld_rng,
- state_local->nrng*sizeof(state_local->ld_rng[0]), MPI_BYTE,
- MASTERRANK(cr), cr->mpi_comm_mygroup);
-#endif
- }
- if (state_local->flags & (1<<estLD_RNGI))
- {
-#ifdef GMX_MPI
- MPI_Gather(state_local->ld_rngi,
- sizeof(state_local->ld_rngi[0]), MPI_BYTE,
- state_global->ld_rngi,
- sizeof(state_local->ld_rngi[0]), MPI_BYTE,
- MASTERRANK(cr), cr->mpi_comm_mygroup);
-#endif
- }
- }
- }
- else
- {
- if (mdof_flags & (MDOF_X | MDOF_XTC))
- {
- MX(state_global->x);
- }
- if (mdof_flags & MDOF_V)
- {
- MX(global_v);
- }
- }
- if (mdof_flags & MDOF_F)
- {
- MX(f_global);
- }
- }
- }
-
- if (MASTER(cr))
- {
- if (mdof_flags & MDOF_CPT)
- {
- write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
- fplog, cr, of->eIntegrator, of->simulation_part,
- of->bExpanded, of->elamstats, step, t, state_global);
- }
-
- if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
- {
- fwrite_trn(of->fp_trn, 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 (gmx_fio_flush(of->fp_trn) != 0)
- {
- gmx_file("Cannot write trajectory; maybe you are out of disk space?");
- }
- gmx_fio_check_file_position(of->fp_trn);
- }
- if (mdof_flags & MDOF_XTC)
- {
- groups = &top_global->groups;
- if (*n_xtc == -1)
- {
- *n_xtc = 0;
- for (i = 0; (i < top_global->natoms); i++)
- {
- if (ggrpnr(groups, egcXTC, i) == 0)
- {
- (*n_xtc)++;
- }
- }
- if (*n_xtc != top_global->natoms)
- {
- snew(*x_xtc, *n_xtc);
- }
- }
- if (*n_xtc == top_global->natoms)
- {
- xxtc = state_global->x;
- }
- else
- {
- xxtc = *x_xtc;
- j = 0;
- for (i = 0; (i < top_global->natoms); i++)
- {
- if (ggrpnr(groups, egcXTC, i) == 0)
- {
- copy_rvec(state_global->x[i], xxtc[j++]);
- }
- }
- }
- if (write_xtc(of->fp_xtc, *n_xtc, step, t,
- state_local->box, xxtc, of->xtc_prec) == 0)
- {
- gmx_fatal(FARGS, "XTC error - maybe you are out of disk space?");
- }
- gmx_fio_check_file_position(of->fp_xtc);
- }
- }
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff