void chk_enx(const char *fn)
{
int nre, fnr, ndr;
ener_file_t in;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr;
gmx_bool bShowTStep;
real t0, old_t1, old_t2;
char buf[22];
fprintf(stderr, "Checking energy file %s\n\n", fn);
in = open_enx(fn, "r");
do_enxnms(in, &nre, &enm);
fprintf(stderr, "%d groups in energy file", nre);
snew(fr, 1);
old_t2 = -2.0;
old_t1 = -1.0;
fnr = 0;
t0 = NOTSET;
bShowTStep = TRUE;
while (do_enx(in, fr))
{
if (fnr >= 2)
{
if (fabs((fr->t-old_t1)-(old_t1-old_t2)) >
0.1*(fabs(fr->t-old_t1)+fabs(old_t1-old_t2)) )
{
bShowTStep = FALSE;
fprintf(stderr, "\nTimesteps at t=%g don't match (%g, %g)\n",
old_t1, old_t1-old_t2, fr->t-old_t1);
}
}
old_t2 = old_t1;
old_t1 = fr->t;
if (t0 == NOTSET)
{
t0 = fr->t;
}
if (fnr == 0)
{
fprintf(stderr, "\rframe: %6s (index %6d), t: %10.3f\n",
gmx_step_str(fr->step, buf), fnr, fr->t);
}
fnr++;
}
fprintf(stderr, "\n\nFound %d frames", fnr);
if (bShowTStep && fnr > 1)
{
fprintf(stderr, " with a timestep of %g ps", (old_t1-t0)/(fnr-1));
}
fprintf(stderr, ".\n");
free_enxframe(fr);
free_enxnms(nre, enm);
sfree(fr);
}
void get_enx_state(char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
t_state *state)
{
/* Should match the names in mdebin.c */
static const char *boxvel_nm[] = {
"Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
"Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
};
static const char *pcouplmu_nm[] = {
"Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
"Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
};
int ind0[] = { XX,YY,ZZ,YY,ZZ,ZZ };
int ind1[] = { XX,YY,ZZ,XX,XX,YY };
int in,nre,nfr,i,ni,npcoupl;
char buf[STRLEN];
gmx_enxnm_t *enm;
t_enxframe *fr;
in = open_enx(fn,"r");
do_enxnms(in,&nre,&enm);
snew(fr,1);
nfr = 0;
while ((nfr==0 || fr->t != t) && do_enx(in,fr)) {
nfr++;
}
close_enx(in);
fprintf(stderr,"\n");
if (nfr == 0 || fr->t != t)
gmx_fatal(FARGS,"Could not find frame with time %f in '%s'",t,fn);
npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
if (ir->epc == epcPARRINELLORAHMAN) {
clear_mat(state->boxv);
for(i=0; i<npcoupl; i++) {
state->boxv[ind0[i]][ind1[i]] =
find_energy(boxvel_nm[i],nre,enm,fr);
}
fprintf(stderr,"\nREAD %d BOX VELOCITIES FROM %s\n\n",npcoupl,fn);
}
if (ir->etc == etcNOSEHOOVER) {
for(i=0; i<state->ngtc; i++) {
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf,"Xi-%s",*(groups->grpname[ni]));
state->nosehoover_xi[i] = find_energy(buf,nre,enm,fr);
}
fprintf(stderr,"\nREAD %d NOSE-HOOVER Xi's FROM %s\n\n",state->ngtc,fn);
}
free_enxnms(nre,enm);
free_enxframe(fr);
sfree(fr);
}
void list_ene(char *fn)
{
int in,ndr;
bool bCont;
t_enxframe *fr;
int i,nre,b;
real rav,minthird;
char **enm=NULL;
printf("gmxdump: %s\n",fn);
in = open_enx(fn,"r");
do_enxnms(in,&nre,&enm);
printf("energy components:\n");
for(i=0; (i<nre); i++)
printf("%5d %s\n",i,enm[i]);
minthird=-1.0/3.0;
snew(fr,1);
do {
bCont=do_enx(in,fr);
if (bCont) {
printf("\n%24s %12.5e %12s %12d\n","time:",
fr->t,"step:",fr->step);
if (fr->nre == nre) {
printf("%24s %12s %12s %12s\n",
"Component","Energy","Av. Energy","Sum Energy");
for(i=0; (i<nre); i++)
printf("%24s %12.5e %12.5e %12.5e\n",
enm[i],fr->ener[i].e,fr->ener[i].eav,fr->ener[i].esum);
}
if (fr->ndisre > 0) {
printf("Distance restraint %8s %8s\n","r(t)","<r^-3>^-3");
for(i=0; i<fr->ndisre; i++) {
rav=pow(fr->disre_rm3tav[i],minthird);
printf("%17d %8.4f %8.4f\n",i,fr->disre_rt[i],rav);
}
}
for(b=0; b<fr->nblock; b++)
if (fr->nr[b] > 0) {
printf("Block data %2d (%4d elm.) %8s\n",b,fr->nr[b],"value");
for(i=0; i<fr->nr[b]; i++)
printf("%24d %8.4f\n",i,fr->block[b][i]);
}
}
} while (bCont);
close_enx(in);
free_enxframe(fr);
sfree(fr);
sfree(enm);
}
void list_ene(const char *fn)
{
int ndr;
ener_file_t in;
gmx_bool bCont;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr;
int i, j, nre, b;
real rav, minthird;
char buf[22];
printf("gmxdump: %s\n", fn);
in = open_enx(fn, "r");
do_enxnms(in, &nre, &enm);
assert(enm);
/*printf("energy components:\n");
for (i = 0; (i < nre); i++)
{
printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit);
}*/
minthird = -1.0/3.0;
snew(fr, 1);
do
{
bCont = do_enx(in, fr);
if (bCont)
{
printf("\n%24s %12.5e %12s %12s\n", "time:",
fr->t, "step:", gmx_step_str(fr->step, buf));
printf("%24s %12s %12s %12s\n",
"", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
printf("%24s %12.5e %12s %12s\n",
"delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
if (fr->nre == nre)
{
printf("%24s %12s %12s %12s\n",
"Component", "Energy", "Av. Energy", "Sum Energy");
if (fr->nsum > 0)
{
for (i = 0; (i < nre); i++)
{
printf("%24s %12.5e %12.5e %12.5e\n",
enm[i].name, fr->ener[i].e, fr->ener[i].eav,
fr->ener[i].esum);
}
}
else
{
for (i = 0; (i < nre); i++)
{
if(fr->ener[i].e != 0)
{
printf("%24s %12.5e\n",
enm[i].name, fr->ener[i].e);
}
}
}
}
for (b = 0; b < fr->nblock; b++)
{
const char *typestr = "";
t_enxblock *eb = &(fr->block[b]);
printf("Block data %2d (%3d subblocks, id=%d)\n",
b, eb->nsub, eb->id);
if (eb->id < enxNR)
{
typestr = enx_block_id_name[eb->id];
}
printf(" id='%s'\n", typestr);
for (i = 0; i < eb->nsub; i++)
{
t_enxsubblock *sb = &(eb->sub[i]);
printf(" Sub block %3d (%5d elems, type=%s) values:\n",
i, sb->nr, xdr_datatype_names[sb->type]);
switch (sb->type)
{
case xdr_datatype_float:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %8.4f\n", j, sb->fval[j]);
}
break;
case xdr_datatype_double:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %10.6f\n", j, sb->dval[j]);
}
break;
case xdr_datatype_int:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %10d\n", j, sb->ival[j]);
}
break;
case xdr_datatype_large_int:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %s\n",
j, gmx_step_str(sb->lval[j], buf));
}
break;
case xdr_datatype_char:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %1c\n", j, sb->cval[j]);
}
break;
case xdr_datatype_string:
for (j = 0; j < sb->nr; j++)
{
printf("%14d %80s\n", j, sb->sval[j]);
}
break;
default:
gmx_incons("Unknown subblock type");
}
}
}
}
}
while (bCont);
close_enx(in);
free_enxframe(fr);
sfree(fr);
sfree(enm);
}
int cmain (int argc, char *argv[])
{
const char *desc[] = {
"tpbconv can edit run input files in four ways.[PAR]",
"[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
"[BB]2.[bb] (OBSOLETE) by creating a run input file",
"for a continuation run when your simulation has crashed due to e.g.",
"a full disk, or by making a continuation run input file.",
"This option is obsolete, since mdrun now writes and reads",
"checkpoint files.",
"[BB]Note[bb] that a frame with coordinates and velocities is needed.",
"When pressure and/or Nose-Hoover temperature coupling is used",
"an energy file can be supplied to get an exact continuation",
"of the original run.[PAR]",
"[BB]3.[bb] by creating a [TT].tpx[tt] file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your [TT].tpx[tt] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [TT].tpx[tt] file.",
"Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this [TT].tpx[tt] file is not fully functional[bb].[PAR]",
"[BB]4.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};
const char *top_fn, *frame_fn;
t_fileio *fp;
ener_file_t fp_ener = NULL;
t_trnheader head;
int i;
gmx_large_int_t nsteps_req, run_step, frame;
double run_t, state_t;
gmx_bool bOK, bNsteps, bExtend, bUntil, bTime, bTraj;
gmx_bool bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState;
gmx_mtop_t mtop;
t_atoms atoms;
t_inputrec *ir, *irnew = NULL;
t_gromppopts *gopts;
t_state state;
rvec *newx = NULL, *newv = NULL, *tmpx, *tmpv;
matrix newbox;
int gnx;
char *grpname;
atom_id *index = NULL;
int nre;
gmx_enxnm_t *enm = NULL;
t_enxframe *fr_ener = NULL;
char buf[200], buf2[200];
output_env_t oenv;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-f", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTPX, "-o", "tpxout", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options */
static int nsteps_req_int = 0;
static real start_t = -1.0, extend_t = 0.0, until_t = 0.0;
static int init_fep_state = 0;
static gmx_bool bContinuation = TRUE, bZeroQ = FALSE, bVel = TRUE;
static t_pargs pa[] = {
{ "-extend", FALSE, etREAL, {&extend_t},
"Extend runtime by this amount (ps)" },
{ "-until", FALSE, etREAL, {&until_t},
"Extend runtime until this ending time (ps)" },
{ "-nsteps", FALSE, etINT, {&nsteps_req_int},
"Change the number of steps" },
{ "-time", FALSE, etREAL, {&start_t},
"Continue from frame at this time (ps) instead of the last frame" },
{ "-zeroq", FALSE, etBOOL, {&bZeroQ},
"Set the charges of a group (from the index) to zero" },
{ "-vel", FALSE, etBOOL, {&bVel},
"Require velocities from trajectory" },
{ "-cont", FALSE, etBOOL, {&bContinuation},
"For exact continuation, the constraints should not be applied before the first step" },
{ "-init_fep_state", FALSE, etINT, {&init_fep_state},
"fep state to initialize from" },
};
int nerror = 0;
CopyRight(stderr, argv[0]);
/* Parse the command line */
parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv);
/* Convert int to gmx_large_int_t */
nsteps_req = nsteps_req_int;
bNsteps = opt2parg_bSet("-nsteps", asize(pa), pa);
bExtend = opt2parg_bSet("-extend", asize(pa), pa);
bUntil = opt2parg_bSet("-until", asize(pa), pa);
bFepState = opt2parg_bSet("-init_fep_state", asize(pa), pa);
bTime = opt2parg_bSet("-time", asize(pa), pa);
bTraj = (opt2bSet("-f", NFILE, fnm) || bTime);
top_fn = ftp2fn(efTPX, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
snew(ir, 1);
read_tpx_state(top_fn, ir, &state, NULL, &mtop);
run_step = ir->init_step;
run_t = ir->init_step*ir->delta_t + ir->init_t;
if (!EI_STATE_VELOCITY(ir->eI))
{
bVel = FALSE;
}
if (bTraj)
{
fprintf(stderr, "\n"
"NOTE: Reading the state from trajectory is an obsolete feature of tpbconv.\n"
" Continuation should be done by loading a checkpoint file with mdrun -cpi\n"
" This guarantees that all state variables are transferred.\n"
" tpbconv is now only useful for increasing nsteps,\n"
" but even that can often be avoided by using mdrun -maxh\n"
"\n");
if (ir->bContinuation != bContinuation)
{
fprintf(stderr, "Modifying ir->bContinuation to %s\n",
bool_names[bContinuation]);
}
ir->bContinuation = bContinuation;
bNeedEner = (ir->epc == epcPARRINELLORAHMAN || ir->etc == etcNOSEHOOVER);
bReadEner = (bNeedEner && ftp2bSet(efEDR, NFILE, fnm));
bScanEner = (bReadEner && !bTime);
if (ir->epc != epcNO || EI_SD(ir->eI) || ir->eI == eiBD)
{
fprintf(stderr, "NOTE: The simulation uses pressure coupling and/or stochastic dynamics.\n"
"tpbconv can not provide binary identical continuation.\n"
"If you want that, supply a checkpoint file to mdrun\n\n");
}
if (EI_SD(ir->eI) || ir->eI == eiBD)
{
fprintf(stderr, "\nChanging ld-seed from %d ", ir->ld_seed);
ir->ld_seed = make_seed();
fprintf(stderr, "to %d\n\n", ir->ld_seed);
}
frame_fn = ftp2fn(efTRN, NFILE, fnm);
if (fn2ftp(frame_fn) == efCPT)
{
int sim_part;
fprintf(stderr,
"\nREADING STATE FROM CHECKPOINT %s...\n\n",
frame_fn);
read_checkpoint_state(frame_fn, &sim_part,
&run_step, &run_t, &state);
}
else
{
fprintf(stderr,
"\nREADING COORDS, VELS AND BOX FROM TRAJECTORY %s...\n\n",
frame_fn);
fp = open_trn(frame_fn, "r");
if (bScanEner)
{
fp_ener = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(fp_ener, &nre, &enm);
snew(fr_ener, 1);
fr_ener->t = -1e-12;
}
/* Now scan until the last set of x and v (step == 0)
* or the ones at step step.
*/
bFrame = TRUE;
frame = 0;
while (bFrame)
{
bFrame = fread_trnheader(fp, &head, &bOK);
if (bOK && frame == 0)
{
if (mtop.natoms != head.natoms)
{
gmx_fatal(FARGS, "Number of atoms in Topology (%d) "
"is not the same as in Trajectory (%d)\n",
mtop.natoms, head.natoms);
}
snew(newx, head.natoms);
snew(newv, head.natoms);
}
bFrame = bFrame && bOK;
if (bFrame)
{
bOK = fread_htrn(fp, &head, newbox, newx, newv, NULL);
}
bFrame = bFrame && bOK;
bUse = FALSE;
if (bFrame &&
(head.x_size) && (head.v_size || !bVel))
{
bUse = TRUE;
if (bScanEner)
{
/* Read until the energy time is >= the trajectory time */
while (fr_ener->t < head.t && do_enx(fp_ener, fr_ener))
{
;
}
bUse = (fr_ener->t == head.t);
}
if (bUse)
{
tmpx = newx;
newx = state.x;
state.x = tmpx;
tmpv = newv;
newv = state.v;
state.v = tmpv;
run_t = head.t;
run_step = head.step;
state.fep_state = head.fep_state;
state.lambda[efptFEP] = head.lambda;
copy_mat(newbox, state.box);
}
}
if (bFrame || !bOK)
{
sprintf(buf, "\r%s %s frame %s%s: step %s%s time %s",
"%s", "%s", "%6", gmx_large_int_fmt, "%6", gmx_large_int_fmt, " %8.3f");
fprintf(stderr, buf,
bUse ? "Read " : "Skipped", ftp2ext(fn2ftp(frame_fn)),
frame, head.step, head.t);
frame++;
if (bTime && (head.t >= start_t))
{
bFrame = FALSE;
}
}
}
if (bScanEner)
{
close_enx(fp_ener);
free_enxframe(fr_ener);
free_enxnms(nre, enm);
}
close_trn(fp);
fprintf(stderr, "\n");
if (!bOK)
{
fprintf(stderr, "%s frame %s (step %s, time %g) is incomplete\n",
ftp2ext(fn2ftp(frame_fn)), gmx_step_str(frame-1, buf2),
gmx_step_str(head.step, buf), head.t);
}
fprintf(stderr, "\nUsing frame of step %s time %g\n",
gmx_step_str(run_step, buf), run_t);
if (bNeedEner)
{
if (bReadEner)
{
get_enx_state(ftp2fn(efEDR, NFILE, fnm), run_t, &mtop.groups, ir, &state);
}
else
{
fprintf(stderr, "\nWARNING: The simulation uses %s temperature and/or %s pressure coupling,\n"
" the continuation will only be exact when an energy file is supplied\n\n",
ETCOUPLTYPE(etcNOSEHOOVER),
EPCOUPLTYPE(epcPARRINELLORAHMAN));
}
}
if (bFepState)
{
ir->fepvals->init_fep_state = init_fep_state;
}
}
}
if (bNsteps)
{
fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(nsteps_req, buf));
ir->nsteps = nsteps_req;
}
else
{
/* Determine total number of steps remaining */
if (bExtend)
{
ir->nsteps = ir->nsteps - (run_step - ir->init_step) + (gmx_large_int_t)(extend_t/ir->delta_t + 0.5);
printf("Extending remaining runtime of by %g ps (now %s steps)\n",
extend_t, gmx_step_str(ir->nsteps, buf));
}
else if (bUntil)
{
printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
gmx_step_str(ir->nsteps, buf),
gmx_step_str(run_step, buf2),
run_t, until_t);
ir->nsteps = (gmx_large_int_t)((until_t - run_t)/ir->delta_t + 0.5);
printf("Extending remaining runtime until %g ps (now %s steps)\n",
until_t, gmx_step_str(ir->nsteps, buf));
}
else
{
ir->nsteps -= run_step - ir->init_step;
/* Print message */
printf("%s steps (%g ps) remaining from first run.\n",
gmx_step_str(ir->nsteps, buf), ir->nsteps*ir->delta_t);
}
}
if (bNsteps || bZeroQ || (ir->nsteps > 0))
{
ir->init_step = run_step;
if (ftp2bSet(efNDX, NFILE, fnm) ||
!(bNsteps || bExtend || bUntil || bTraj))
{
atoms = gmx_mtop_global_atoms(&mtop);
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1,
&gnx, &index, &grpname);
if (!bZeroQ)
{
bSel = (gnx != state.natoms);
for (i = 0; ((i < gnx) && (!bSel)); i++)
{
bSel = (i != index[i]);
}
}
else
{
bSel = FALSE;
}
if (bSel)
{
fprintf(stderr, "Will write subset %s of original tpx containing %d "
"atoms\n", grpname, gnx);
reduce_topology_x(gnx, index, &mtop, state.x, state.v);
state.natoms = gnx;
}
else if (bZeroQ)
{
zeroq(gnx, index, &mtop);
fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
}
else
{
fprintf(stderr, "Will write full tpx file (no selection)\n");
}
}
state_t = ir->init_t + ir->init_step*ir->delta_t;
sprintf(buf, "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10", gmx_large_int_fmt, "%10", gmx_large_int_fmt);
fprintf(stderr, buf, ir->init_step, ir->nsteps);
fprintf(stderr, " time %10.3f and length %10.3f ps\n",
state_t, ir->nsteps*ir->delta_t);
write_tpx_state(opt2fn("-o", NFILE, fnm), ir, &state, &mtop);
}
else
{
printf("You've simulated long enough. Not writing tpr file\n");
}
thanx(stderr);
return 0;
}
void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
FILE *log,
gmx_int64_t step, double time,
int mode,
t_mdebin *md, t_fcdata *fcd,
gmx_groups_t *groups, t_grpopts *opts)
{
/*static char **grpnms=NULL;*/
char buf[246];
int i, j, n, ni, nj, b;
int ndisre = 0;
real *disre_rm3tav, *disre_rt;
/* these are for the old-style blocks (1 subblock, only reals), because
there can be only one per ID for these */
int nr[enxNR];
int id[enxNR];
real *block[enxNR];
t_enxframe fr;
switch (mode)
{
case eprNORMAL:
init_enxframe(&fr);
fr.t = time;
fr.step = step;
fr.nsteps = md->ebin->nsteps;
fr.dt = md->delta_t;
fr.nsum = md->ebin->nsum;
fr.nre = (bEne) ? md->ebin->nener : 0;
fr.ener = md->ebin->e;
ndisre = bDR ? fcd->disres.npair : 0;
disre_rm3tav = fcd->disres.rm3tav;
disre_rt = fcd->disres.rt;
/* Optional additional old-style (real-only) blocks. */
for (i = 0; i < enxNR; i++)
{
nr[i] = 0;
}
if (fcd->orires.nr > 0 && bOR)
{
diagonalize_orires_tensors(&(fcd->orires));
nr[enxOR] = fcd->orires.nr;
block[enxOR] = fcd->orires.otav;
id[enxOR] = enxOR;
nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
fcd->orires.nr : 0;
block[enxORI] = fcd->orires.oinsl;
id[enxORI] = enxORI;
nr[enxORT] = fcd->orires.nex*12;
block[enxORT] = fcd->orires.eig;
id[enxORT] = enxORT;
}
/* whether we are going to wrte anything out: */
if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
{
/* the old-style blocks go first */
fr.nblock = 0;
for (i = 0; i < enxNR; i++)
{
if (nr[i] > 0)
{
fr.nblock = i + 1;
}
}
add_blocks_enxframe(&fr, fr.nblock);
for (b = 0; b < fr.nblock; b++)
{
add_subblocks_enxblock(&(fr.block[b]), 1);
fr.block[b].id = id[b];
fr.block[b].sub[0].nr = nr[b];
#if !GMX_DOUBLE
fr.block[b].sub[0].type = xdr_datatype_float;
fr.block[b].sub[0].fval = block[b];
#else
fr.block[b].sub[0].type = xdr_datatype_double;
fr.block[b].sub[0].dval = block[b];
#endif
}
/* check for disre block & fill it. */
if (ndisre > 0)
{
int db = fr.nblock;
fr.nblock += 1;
add_blocks_enxframe(&fr, fr.nblock);
add_subblocks_enxblock(&(fr.block[db]), 2);
fr.block[db].id = enxDISRE;
fr.block[db].sub[0].nr = ndisre;
fr.block[db].sub[1].nr = ndisre;
#if !GMX_DOUBLE
fr.block[db].sub[0].type = xdr_datatype_float;
fr.block[db].sub[1].type = xdr_datatype_float;
fr.block[db].sub[0].fval = disre_rt;
fr.block[db].sub[1].fval = disre_rm3tav;
#else
fr.block[db].sub[0].type = xdr_datatype_double;
fr.block[db].sub[1].type = xdr_datatype_double;
fr.block[db].sub[0].dval = disre_rt;
fr.block[db].sub[1].dval = disre_rm3tav;
#endif
}
/* here we can put new-style blocks */
/* Free energy perturbation blocks */
if (md->dhc)
{
mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
}
/* we can now free & reset the data in the blocks */
if (md->dhc)
{
mde_delta_h_coll_reset(md->dhc);
}
/* do the actual I/O */
do_enx(fp_ene, &fr);
if (fr.nre)
{
/* We have stored the sums, so reset the sum history */
reset_ebin_sums(md->ebin);
}
}
free_enxframe(&fr);
break;
case eprAVER:
if (log)
{
pprint(log, "A V E R A G E S", md);
}
break;
case eprRMS:
if (log)
{
pprint(log, "R M S - F L U C T U A T I O N S", md);
}
break;
default:
gmx_fatal(FARGS, "Invalid print mode (%d)", mode);
}
if (log)
{
for (i = 0; i < opts->ngtc; i++)
{
if (opts->annealing[i] != eannNO)
{
fprintf(log, "Current ref_t for group %s: %8.1f\n",
*(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
opts->ref_t[i]);
}
}
if (mode == eprNORMAL && fcd->orires.nr > 0)
{
print_orires_log(log, &(fcd->orires));
}
fprintf(log, " Energies (%s)\n", unit_energy);
pr_ebin(log, md->ebin, md->ie, md->f_nre+md->nCrmsd, 5, mode, TRUE);
fprintf(log, "\n");
if (mode == eprAVER)
{
if (md->bDynBox)
{
pr_ebin(log, md->ebin, md->ib, md->bTricl ? NTRICLBOXS : NBOXS, 5,
mode, TRUE);
fprintf(log, "\n");
}
if (md->bConstrVir)
{
fprintf(log, " Constraint Virial (%s)\n", unit_energy);
pr_ebin(log, md->ebin, md->isvir, 9, 3, mode, FALSE);
fprintf(log, "\n");
fprintf(log, " Force Virial (%s)\n", unit_energy);
pr_ebin(log, md->ebin, md->ifvir, 9, 3, mode, FALSE);
fprintf(log, "\n");
}
fprintf(log, " Total Virial (%s)\n", unit_energy);
pr_ebin(log, md->ebin, md->ivir, 9, 3, mode, FALSE);
fprintf(log, "\n");
fprintf(log, " Pressure (%s)\n", unit_pres_bar);
pr_ebin(log, md->ebin, md->ipres, 9, 3, mode, FALSE);
fprintf(log, "\n");
if (md->bMu)
{
fprintf(log, " Total Dipole (%s)\n", unit_dipole_D);
pr_ebin(log, md->ebin, md->imu, 3, 3, mode, FALSE);
fprintf(log, "\n");
}
if (md->nE > 1)
{
if (md->print_grpnms == NULL)
{
snew(md->print_grpnms, md->nE);
n = 0;
for (i = 0; (i < md->nEg); i++)
{
ni = groups->grps[egcENER].nm_ind[i];
for (j = i; (j < md->nEg); j++)
{
nj = groups->grps[egcENER].nm_ind[j];
sprintf(buf, "%s-%s", *(groups->grpname[ni]),
*(groups->grpname[nj]));
md->print_grpnms[n++] = gmx_strdup(buf);
}
}
}
sprintf(buf, "Epot (%s)", unit_energy);
fprintf(log, "%15s ", buf);
for (i = 0; (i < egNR); i++)
{
if (md->bEInd[i])
{
fprintf(log, "%12s ", egrp_nm[i]);
}
}
fprintf(log, "\n");
for (i = 0; (i < md->nE); i++)
{
fprintf(log, "%15s", md->print_grpnms[i]);
pr_ebin(log, md->ebin, md->igrp[i], md->nEc, md->nEc, mode,
FALSE);
}
fprintf(log, "\n");
}
if (md->nTC > 1)
{
pr_ebin(log, md->ebin, md->itemp, md->nTC, 4, mode, TRUE);
fprintf(log, "\n");
}
if (md->nU > 1)
{
fprintf(log, "%15s %12s %12s %12s\n",
"Group", "Ux", "Uy", "Uz");
for (i = 0; (i < md->nU); i++)
{
ni = groups->grps[egcACC].nm_ind[i];
fprintf(log, "%15s", *groups->grpname[ni]);
pr_ebin(log, md->ebin, md->iu+3*i, 3, 3, mode, FALSE);
}
fprintf(log, "\n");
}
}
}
}
int open_enx(char *fn,char *mode)
{
int fp,nre,i;
char **nm=NULL;
t_enxframe *fr;
bool bDum=TRUE;
/* Energy files should always be opened as binary files,
* but that is checked in gmx_fio_open.
*/
if (mode[0]=='r') {
fp=gmx_fio_open(fn,mode);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,FALSE);
do_enxnms(fp,&nre,&nm);
snew(fr,1);
do_eheader(fp,fr,&bDum);
/* Now check whether this file is in single precision */
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(float) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(float)*2+sizeof(int) == fr->d_size)))){
fprintf(stderr,"Opened %s as single precision energy file\n",fn);
for(i=0; (i<nre); i++)
sfree(nm[i]);
sfree(nm);
}
else {
gmx_fio_rewind(fp);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,TRUE);
do_enxnms(fp,&nre,&nm);
do_eheader(fp,fr,&bDum);
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(double) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(double)*2+sizeof(int) == fr->d_size))))
fprintf(stderr,"Opened %s as double precision energy file\n",fn);
else {
if (empty_file(fn))
fatal_error(0,"File %s is empty",fn);
else
fatal_error(0,"Energy file %s not recognized, maybe different CPU?",
fn);
}
for(i=0; (i<nre); i++)
sfree(nm[i]);
sfree(nm);
}
free_enxframe(fr);
sfree(fr);
gmx_fio_rewind(fp);
}
else
fp = gmx_fio_open(fn,mode);
framenr=0;
return fp;
}
ener_file_t open_enx(const char *fn,const char *mode)
{
int nre,i;
gmx_enxnm_t *nms=NULL;
int file_version=-1;
t_enxframe *fr;
gmx_bool bWrongPrecision,bOK=TRUE;
struct ener_file *ef;
snew(ef,1);
if (mode[0]=='r') {
ef->fio=gmx_fio_open(fn,mode);
gmx_fio_checktype(ef->fio);
gmx_fio_setprecision(ef->fio,FALSE);
do_enxnms(ef,&nre,&nms);
snew(fr,1);
do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
if(!bOK)
{
gmx_file("Cannot read energy file header. Corrupt file?");
}
/* Now check whether this file is in single precision */
if (!bWrongPrecision &&
((fr->e_size && (fr->nre == nre) &&
(nre*4*(long int)sizeof(float) == fr->e_size)) ) )
{
fprintf(stderr,"Opened %s as single precision energy file\n",fn);
free_enxnms(nre,nms);
}
else
{
gmx_fio_rewind(ef->fio);
gmx_fio_checktype(ef->fio);
gmx_fio_setprecision(ef->fio,TRUE);
do_enxnms(ef,&nre,&nms);
do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
if(!bOK)
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*(long int)sizeof(double) == fr->e_size)) ))
fprintf(stderr,"Opened %s as double precision energy file\n",
fn);
else {
if (empty_file(fn))
gmx_fatal(FARGS,"File %s is empty",fn);
else
gmx_fatal(FARGS,"Energy file %s not recognized, maybe different CPU?",
fn);
}
free_enxnms(nre,nms);
}
free_enxframe(fr);
sfree(fr);
gmx_fio_rewind(ef->fio);
}
else
ef->fio = gmx_fio_open(fn,mode);
ef->framenr=0;
ef->frametime=0;
return ef;
}
void get_enx_state(const char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
t_state *state)
{
/* Should match the names in mdebin.c */
static const char *boxvel_nm[] = {
"Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
"Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
};
static const char *pcouplmu_nm[] = {
"Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
"Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
};
static const char *baro_nm[] = {
"Barostat"
};
int ind0[] = { XX,YY,ZZ,YY,ZZ,ZZ };
int ind1[] = { XX,YY,ZZ,XX,XX,YY };
int nre,nfr,i,j,ni,npcoupl;
char buf[STRLEN];
const char *bufi;
gmx_enxnm_t *enm=NULL;
t_enxframe *fr;
ener_file_t in;
in = open_enx(fn,"r");
do_enxnms(in,&nre,&enm);
snew(fr,1);
nfr = 0;
while ((nfr==0 || fr->t != t) && do_enx(in,fr)) {
nfr++;
}
close_enx(in);
fprintf(stderr,"\n");
if (nfr == 0 || fr->t != t)
gmx_fatal(FARGS,"Could not find frame with time %f in '%s'",t,fn);
npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
if (ir->epc == epcPARRINELLORAHMAN) {
clear_mat(state->boxv);
for(i=0; i<npcoupl; i++) {
state->boxv[ind0[i]][ind1[i]] =
find_energy(boxvel_nm[i],nre,enm,fr);
}
fprintf(stderr,"\nREAD %d BOX VELOCITIES FROM %s\n\n",npcoupl,fn);
}
if (ir->etc == etcNOSEHOOVER)
{
for(i=0; i<state->ngtc; i++) {
ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
for(j=0; (j<state->nhchainlength); j++)
{
sprintf(buf,"Xi-%d-%s",j,bufi);
state->nosehoover_xi[i] = find_energy(buf,nre,enm,fr);
sprintf(buf,"vXi-%d-%s",j,bufi);
state->nosehoover_vxi[i] = find_energy(buf,nre,enm,fr);
}
}
fprintf(stderr,"\nREAD %d NOSE-HOOVER Xi chains FROM %s\n\n",state->ngtc,fn);
if (IR_NPT_TROTTER(ir))
{
for(i=0; i<state->nnhpres; i++) {
bufi = baro_nm[0]; /* All barostat DOF's together for now */
for(j=0; (j<state->nhchainlength); j++)
{
sprintf(buf,"Xi-%d-%s",j,bufi);
state->nhpres_xi[i] = find_energy(buf,nre,enm,fr);
sprintf(buf,"vXi-%d-%s",j,bufi);
state->nhpres_vxi[i] = find_energy(buf,nre,enm,fr);
}
}
fprintf(stderr,"\nREAD %d NOSE-HOOVER BAROSTAT Xi chains FROM %s\n\n",state->nnhpres,fn);
}
}
free_enxnms(nre,enm);
free_enxframe(fr);
sfree(fr);
}
static int scan_ene_files(char **fnms, int nfiles,
real *readtime, real *timestep, int *nremax)
{
/* Check number of energy terms and start time of all files */
int f, nre, nremin = 0, nresav = 0;
ener_file_t in;
real t1, t2;
char inputstring[STRLEN];
gmx_enxnm_t *enm;
t_enxframe *fr;
snew(fr, 1);
for (f = 0; f < nfiles; f++)
{
in = open_enx(fnms[f], "r");
enm = NULL;
do_enxnms(in, &nre, &enm);
if (f == 0)
{
nresav = nre;
nremin = nre;
*nremax = nre;
do_enx(in, fr);
t1 = fr->t;
do_enx(in, fr);
t2 = fr->t;
*timestep = t2-t1;
readtime[f] = t1;
close_enx(in);
}
else
{
nremin = std::min(nremin, fr->nre);
*nremax = std::max(*nremax, fr->nre);
if (nre != nresav)
{
fprintf(stderr,
"Energy files don't match, different number of energies:\n"
" %s: %d\n %s: %d\n", fnms[f-1], nresav, fnms[f], fr->nre);
fprintf(stderr,
"\nContinue conversion using only the first %d terms (n/y)?\n"
"(you should be sure that the energy terms match)\n", nremin);
if (NULL == fgets(inputstring, STRLEN-1, stdin))
{
gmx_fatal(FARGS, "Error reading user input");
}
if (inputstring[0] != 'y' && inputstring[0] != 'Y')
{
fprintf(stderr, "Will not convert\n");
exit(0);
}
nresav = fr->nre;
}
do_enx(in, fr);
readtime[f] = fr->t;
close_enx(in);
}
fprintf(stderr, "\n");
free_enxnms(nre, enm);
}
free_enxframe(fr);
sfree(fr);
return nremin;
}
int open_enx(const char *fn,const char *mode)
{
int fp,nre,i;
gmx_enxnm_t *nms=NULL;
int file_version=-1;
t_enxframe *fr;
bool bDum=TRUE;
if (mode[0]=='r') {
fp=gmx_fio_open(fn,mode);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,FALSE);
do_enxnms(fp,&nre,&nms);
snew(fr,1);
do_eheader(fp,&file_version,fr,TRUE,&bDum);
if(!bDum)
{
gmx_file("Cannot read energy file header. Corrupt file?");
}
/* Now check whether this file is in single precision */
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(float) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(float)*2+sizeof(int) == fr->d_size)))){
fprintf(stderr,"Opened %s as single precision energy file\n",fn);
free_enxnms(nre,nms);
}
else {
gmx_fio_rewind(fp);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,TRUE);
do_enxnms(fp,&nre,&nms);
do_eheader(fp,&file_version,fr,TRUE,&bDum);
if(!bDum)
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(double) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(double)*2+sizeof(int) == fr->d_size))))
fprintf(stderr,"Opened %s as double precision energy file\n",fn);
else {
if (empty_file(fn))
gmx_fatal(FARGS,"File %s is empty",fn);
else
gmx_fatal(FARGS,"Energy file %s not recognized, maybe different CPU?",
fn);
}
free_enxnms(nre,nms);
}
free_enxframe(fr);
sfree(fr);
gmx_fio_rewind(fp);
}
else
fp = gmx_fio_open(fn,mode);
framenr=0;
frametime=0;
return fp;
}
void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener)
{
int nre, nre1, nre2;
ener_file_t in1, in2;
int i, j, maxener, *ind1, *ind2, *have;
gmx_enxnm_t *enm1 = NULL, *enm2 = NULL;
t_enxframe *fr1, *fr2;
gmx_bool b1, b2;
fprintf(stdout, "comparing energy file %s and %s\n\n", fn1, fn2);
in1 = open_enx(fn1, "r");
in2 = open_enx(fn2, "r");
do_enxnms(in1, &nre1, &enm1);
do_enxnms(in2, &nre2, &enm2);
if (nre1 != nre2)
{
fprintf(stdout, "There are %d and %d terms in the energy files\n\n",
nre1, nre2);
}
else
{
fprintf(stdout, "There are %d terms in the energy files\n\n", nre1);
}
snew(ind1, nre1);
snew(ind2, nre2);
snew(have, nre2);
nre = 0;
for (i = 0; i < nre1; i++)
{
for (j = 0; j < nre2; j++)
{
if (enernm_equal(enm1[i].name, enm2[j].name))
{
ind1[nre] = i;
ind2[nre] = j;
have[j] = 1;
nre++;
break;
}
}
if (nre == 0 || ind1[nre-1] != i)
{
cmp_str(stdout, "enm", i, enm1[i].name, "-");
}
}
for (i = 0; i < nre2; i++)
{
if (have[i] == 0)
{
cmp_str(stdout, "enm", i, "-", enm2[i].name);
}
}
maxener = nre;
for (i = 0; i < nre; i++)
{
if ((lastener != NULL) && (std::strstr(enm1[i].name, lastener) != NULL))
{
maxener = i+1;
break;
}
}
fprintf(stdout, "There are %d terms to compare in the energy files\n\n",
maxener);
for (i = 0; i < maxener; i++)
{
cmp_str(stdout, "unit", i, enm1[ind1[i]].unit, enm2[ind2[i]].unit);
}
snew(fr1, 1);
snew(fr2, 1);
do
{
b1 = do_enx(in1, fr1);
b2 = do_enx(in2, fr2);
if (b1 && !b2)
{
fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn2, fn1);
}
else if (!b1 && b2)
{
fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn1, fn2);
}
else if (!b1 && !b2)
{
fprintf(stdout, "\nFiles read successfully\n");
}
else
{
cmp_real(stdout, "t", -1, fr1->t, fr2->t, ftol, abstol);
cmp_int(stdout, "step", -1, fr1->step, fr2->step);
/* We don't want to print the nre mismatch for every frame */
/* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */
if ((fr1->nre >= nre) && (fr2->nre >= nre))
{
cmp_energies(stdout, fr1->step, fr1->step, fr1->ener, fr2->ener,
enm1, ftol, abstol, nre, ind1, ind2, maxener);
}
/*cmp_disres(fr1,fr2,ftol,abstol);*/
cmp_eblocks(fr1, fr2, ftol, abstol);
}
}
while (b1 && b2);
close_enx(in1);
close_enx(in2);
free_enxframe(fr2);
sfree(fr2);
free_enxframe(fr1);
sfree(fr1);
}
//! Helper function to clean up resources
void done_enxframe(t_enxframe *fr)
{
// Free the contents, then the pointer itself
free_enxframe(fr);
sfree(fr);
}
