/* The function used for spawning threads. Extracts the mdrunner()
arguments from its one argument and calls mdrunner(), after making
a commrec. */
static void mdrunner_start_fn(void *arg)
{
struct mdrunner_arglist *mda = (struct mdrunner_arglist*)arg;
struct mdrunner_arglist mc = *mda; /* copy the arg list to make sure
that it's thread-local. This doesn't
copy pointed-to items, of course,
but those are all const. */
t_commrec *cr; /* we need a local version of this */
FILE *fplog = NULL;
t_filenm *fnm;
fnm = dup_tfn(mc.nfile, mc.fnm);
cr = reinitialize_commrec_for_this_thread(mc.cr);
if (MASTER(cr))
{
fplog = mc.fplog;
}
mdrunner(&mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
mc.ddxyz, mc.dd_node_order, mc.rdd,
mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
mc.ddcsx, mc.ddcsy, mc.ddcsz,
mc.nbpu_opt, mc.nstlist_cmdline,
mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
mc.cpt_period, mc.max_hours, mc.imdport, mc.Flags);
}
int gmx_sans(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes SANS spectra using Debye formula.",
"It currently uses topology file (since it need to assigne element for each atom).",
"[PAR]",
"Parameters:[PAR]"
"[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
"[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
"[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
"[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
"[TT]-startq[tt] Starting q value in nm[PAR]",
"[TT]-endq[tt] Ending q value in nm[PAR]",
"[TT]-qstep[tt] Stepping in q space[PAR]",
"Note: When using Debye direct method computational cost increases as",
"1/2 * N * (N - 1) where N is atom number in group of interest.",
"[PAR]",
"WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
};
static gmx_bool bPBC = TRUE;
static gmx_bool bNORM = FALSE;
static real binwidth = 0.2, grid = 0.05; /* bins shouldnt be smaller then smallest bond (~0.1nm) length */
static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
static real mcover = -1;
static unsigned int seed = 0;
static int nthreads = -1;
static const char *emode[] = { NULL, "direct", "mc", NULL };
static const char *emethod[] = { NULL, "debye", "fft", NULL };
gmx_neutron_atomic_structurefactors_t *gnsf;
gmx_sans_t *gsans;
#define NPA asize(pa)
t_pargs pa[] = {
{ "-bin", FALSE, etREAL, {&binwidth},
"[HIDDEN]Binwidth (nm)" },
{ "-mode", FALSE, etENUM, {emode},
"Mode for sans spectra calculation" },
{ "-mcover", FALSE, etREAL, {&mcover},
"Monte-Carlo coverage should be -1(default) or (0,1]"},
{ "-method", FALSE, etENUM, {emethod},
"[HIDDEN]Method for sans spectra calculation" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions for computing distances" },
{ "-grid", FALSE, etREAL, {&grid},
"[HIDDEN]Grid spacing (in nm) for FFTs" },
{"-startq", FALSE, etREAL, {&start_q},
"Starting q (1/nm) "},
{"-endq", FALSE, etREAL, {&end_q},
"Ending q (1/nm)"},
{ "-qstep", FALSE, etREAL, {&q_step},
"Stepping in q (1/nm)"},
{ "-seed", FALSE, etINT, {&seed},
"Random seed for Monte-Carlo"},
#ifdef GMX_OPENMP
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to start"},
#endif
};
FILE *fp;
const char *fnTPX, *fnNDX, *fnTRX, *fnDAT = NULL;
t_trxstatus *status;
t_topology *top = NULL;
t_atom *atom = NULL;
gmx_rmpbc_t gpbc = NULL;
gmx_bool bTPX;
gmx_bool bFFT = FALSE, bDEBYE = FALSE;
gmx_bool bMC = FALSE;
int ePBC = -1;
matrix box;
char title[STRLEN];
rvec *x;
int natoms;
real t;
char **grpname = NULL;
atom_id *index = NULL;
int isize;
int i, j;
char *hdr = NULL;
char *suffix = NULL;
t_filenm *fnmdup = NULL;
gmx_radial_distribution_histogram_t *prframecurrent = NULL, *pr = NULL;
gmx_static_structurefactor_t *sqframecurrent = NULL, *sq = NULL;
output_env_t oenv;
#define NFILE asize(fnm)
t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-d", "nsfactor", ffOPTRD },
{ efXVG, "-pr", "pr", ffWRITE },
{ efXVG, "-sq", "sq", ffWRITE },
{ efXVG, "-prframe", "prframe", ffOPTWR },
{ efXVG, "-sqframe", "sqframe", ffOPTWR }
};
nthreads = gmx_omp_get_max_threads();
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* check that binwidth not smaller than smallers distance */
check_binwidth(binwidth);
check_mcover(mcover);
/* setting number of omp threads globaly */
gmx_omp_set_num_threads(nthreads);
/* Now try to parse opts for modes */
switch (emethod[0][0])
{
case 'd':
bDEBYE = TRUE;
switch (emode[0][0])
{
case 'd':
bMC = FALSE;
break;
case 'm':
bMC = TRUE;
break;
default:
break;
}
break;
case 'f':
bFFT = TRUE;
break;
default:
break;
}
if (bDEBYE)
{
if (bMC)
{
fprintf(stderr, "Using Monte Carlo Debye method to calculate spectrum\n");
}
else
{
fprintf(stderr, "Using direct Debye method to calculate spectrum\n");
}
}
else if (bFFT)
{
gmx_fatal(FARGS, "FFT method not implemented!");
}
else
{
gmx_fatal(FARGS, "Unknown combination for mode and method!");
}
/* Try to read files */
fnDAT = ftp2fn(efDAT, NFILE, fnm);
fnTPX = ftp2fn(efTPX, NFILE, fnm);
fnTRX = ftp2fn(efTRX, NFILE, fnm);
gnsf = gmx_neutronstructurefactors_init(fnDAT);
fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
snew(top, 1);
snew(grpname, 1);
snew(index, 1);
bTPX = read_tps_conf(fnTPX, title, top, &ePBC, &x, NULL, box, TRUE);
printf("\nPlease select group for SANS spectra calculation:\n");
get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
gsans = gmx_sans_init(top, gnsf);
/* Prepare reference frame */
if (bPBC)
{
gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
gmx_rmpbc(gpbc, top->atoms.nr, box, x);
}
natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
if (natoms != top->atoms.nr)
{
fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
}
do
{
if (bPBC)
{
gmx_rmpbc(gpbc, top->atoms.nr, box, x);
}
/* allocate memory for pr */
if (pr == NULL)
{
/* in case its first frame to read */
snew(pr, 1);
}
/* realy calc p(r) */
prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
/* copy prframecurrent -> pr and summ up pr->gr[i] */
/* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
if (pr->gr == NULL)
{
/* check if we use pr->gr first time */
snew(pr->gr, prframecurrent->grn);
snew(pr->r, prframecurrent->grn);
}
else
{
/* resize pr->gr and pr->r if needed to preven overruns */
if (prframecurrent->grn > pr->grn)
{
srenew(pr->gr, prframecurrent->grn);
srenew(pr->r, prframecurrent->grn);
}
}
pr->grn = prframecurrent->grn;
pr->binwidth = prframecurrent->binwidth;
/* summ up gr and fill r */
for (i = 0; i < prframecurrent->grn; i++)
{
pr->gr[i] += prframecurrent->gr[i];
pr->r[i] = prframecurrent->r[i];
}
/* normalize histo */
normalize_probability(prframecurrent->grn, prframecurrent->gr);
/* convert p(r) to sq */
sqframecurrent = convert_histogram_to_intensity_curve(prframecurrent, start_q, end_q, q_step);
/* print frame data if needed */
if (opt2fn_null("-prframe", NFILE, fnm))
{
snew(hdr, 25);
snew(suffix, GMX_PATH_MAX);
/* prepare header */
sprintf(hdr, "g(r), t = %f", t);
/* prepare output filename */
fnmdup = dup_tfn(NFILE, fnm);
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup, NFILE, suffix);
fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup), hdr, "Distance (nm)", "Probability", oenv);
for (i = 0; i < prframecurrent->grn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
}
done_filenms(NFILE, fnmdup);
fclose(fp);
sfree(hdr);
sfree(suffix);
sfree(fnmdup);
}
if (opt2fn_null("-sqframe", NFILE, fnm))
{
snew(hdr, 25);
snew(suffix, GMX_PATH_MAX);
/* prepare header */
sprintf(hdr, "I(q), t = %f", t);
/* prepare output filename */
fnmdup = dup_tfn(NFILE, fnm);
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup, NFILE, suffix);
fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
for (i = 0; i < sqframecurrent->qn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
}
done_filenms(NFILE, fnmdup);
fclose(fp);
sfree(hdr);
sfree(suffix);
sfree(fnmdup);
}
/* free pr structure */
sfree(prframecurrent->gr);
sfree(prframecurrent->r);
sfree(prframecurrent);
/* free sq structure */
sfree(sqframecurrent->q);
sfree(sqframecurrent->s);
sfree(sqframecurrent);
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
/* normalize histo */
normalize_probability(pr->grn, pr->gr);
sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
/* prepare pr.xvg */
fp = xvgropen(opt2fn_null("-pr", NFILE, fnm), "G(r)", "Distance (nm)", "Probability", oenv);
for (i = 0; i < pr->grn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
}
xvgrclose(fp);
/* prepare sq.xvg */
fp = xvgropen(opt2fn_null("-sq", NFILE, fnm), "I(q)", "q (nm^-1)", "s(q)/s(0)", oenv);
for (i = 0; i < sq->qn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
}
xvgrclose(fp);
/*
* Clean up memory
*/
sfree(pr->gr);
sfree(pr->r);
sfree(pr);
sfree(sq->q);
sfree(sq->s);
sfree(sq);
please_cite(stdout, "Garmay2012");
return 0;
}
/* called by mdrunner() to start a specific number of threads (including
the main thread) for thread-parallel runs. This in turn calls mdrunner()
for each thread.
All options besides nthreads are the same as for mdrunner(). */
static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
FILE *fplog, t_commrec *cr, int nfile,
const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
gmx_bool bCompact, int nstglobalcomm,
ivec ddxyz, int dd_node_order, real rdd, real rconstr,
const char *dddlb_opt, real dlb_scale,
const char *ddcsx, const char *ddcsy, const char *ddcsz,
const char *nbpu_opt, int nstlist_cmdline,
gmx_int64_t nsteps_cmdline,
int nstepout, int resetstep,
int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
real pforce, real cpt_period, real max_hours,
unsigned long Flags)
{
int ret;
struct mdrunner_arglist *mda;
t_commrec *crn; /* the new commrec */
t_filenm *fnmn;
/* first check whether we even need to start tMPI */
if (hw_opt->nthreads_tmpi < 2)
{
return cr;
}
/* a few small, one-time, almost unavoidable memory leaks: */
snew(mda, 1);
fnmn = dup_tfn(nfile, fnm);
/* fill the data structure to pass as void pointer to thread start fn */
/* hw_opt contains pointers, which should all be NULL at this stage */
mda->hw_opt = *hw_opt;
mda->fplog = fplog;
mda->cr = cr;
mda->nfile = nfile;
mda->fnm = fnmn;
mda->oenv = oenv;
mda->bVerbose = bVerbose;
mda->bCompact = bCompact;
mda->nstglobalcomm = nstglobalcomm;
mda->ddxyz[XX] = ddxyz[XX];
mda->ddxyz[YY] = ddxyz[YY];
mda->ddxyz[ZZ] = ddxyz[ZZ];
mda->dd_node_order = dd_node_order;
mda->rdd = rdd;
mda->rconstr = rconstr;
mda->dddlb_opt = dddlb_opt;
mda->dlb_scale = dlb_scale;
mda->ddcsx = ddcsx;
mda->ddcsy = ddcsy;
mda->ddcsz = ddcsz;
mda->nbpu_opt = nbpu_opt;
mda->nstlist_cmdline = nstlist_cmdline;
mda->nsteps_cmdline = nsteps_cmdline;
mda->nstepout = nstepout;
mda->resetstep = resetstep;
mda->nmultisim = nmultisim;
mda->repl_ex_nst = repl_ex_nst;
mda->repl_ex_nex = repl_ex_nex;
mda->repl_ex_seed = repl_ex_seed;
mda->pforce = pforce;
mda->cpt_period = cpt_period;
mda->max_hours = max_hours;
mda->Flags = Flags;
/* now spawn new threads that start mdrunner_start_fn(), while
the main thread returns, we set thread affinity later */
ret = tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi, TMPI_AFFINITY_NONE,
mdrunner_start_fn, (void*)(mda) );
if (ret != TMPI_SUCCESS)
{
return NULL;
}
crn = reinitialize_commrec_for_this_thread(cr);
return crn;
}