static void setup_aster_kalman(SIM_S *simu, ASTER_S *aster, STAR_S *star, const PARMS_S *parms){
int ndtrat=parms->skyc.ndtrat;
if(parms->skyc.multirate){
aster->res_ngs=dnew(1,1);
//assemble neam
if(aster->neam) error("neam is already set?\n");
aster->neam=calloc(1, sizeof(dcell*));
aster->neam[0]=cellnew(aster->nwfs, aster->nwfs);
for(int iwfs=0; iwfs<aster->nwfs; iwfs++){
int ng=aster->g->p[iwfs]->nx;
aster->neam[0]->p[iwfs+aster->nwfs*iwfs]=dnew(ng, ng);
}
aster->dtrats=dnew(aster->nwfs, 1);
aster->idtrats=dnew(aster->nwfs, 1);
int wfs0_min=0, wfs0_max=0;
PISTAT_S *pistat0=&star[aster->wfs[0].istar].pistat[aster->wfs[0].ipowfs];
for(int idtrat=0; idtrat<parms->skyc.ndtrat; idtrat++){
if(wfs0_min==0 && pistat0->snr->p[idtrat]>3){
wfs0_min=idtrat;
}
if(pistat0->snr->p[idtrat]>=parms->skyc.snrmin->p[idtrat]){
wfs0_max=idtrat;
}
}
aster->kalman=calloc(1, sizeof(kalman_t*));
double resmin=INFINITY;
kalman_t *kalman_min=0;
int idtrat_min=0;
//Try progressively lower sampling frequencies until performance starts to degrades
for(int idtrat_limit=wfs0_max; idtrat_limit>wfs0_min; idtrat_limit--){
setup_aster_kalman_dtrat(aster, star, parms, idtrat_limit);
aster->kalman[0]=sde_kalman(simu->sdecoeff, parms->maos.dt, aster->dtrats, aster->g, aster->neam[0], 0);
dmat *rests=0;
#if 1 //more accurate
dmat *res=skysim_sim(parms->skyc.dbg?&rests:0, simu->mideal, simu->mideal_oa, simu->rmsol,
aster, 0, parms, -1, 1, -1);
double res0=res?res->p[0]:simu->rmsol;
dfree(res);
#else
rests=kalman_test(aster->kalman[0], simu->mideal);
double res0=calc_rms(rests, parms->maos.mcc, parms->skyc.evlstart);
#endif
if(parms->skyc.dbg){
writebin(rests, "isky%d_iaster%d_dtrat%d_rest", simu->isky, aster->iaster, idtrat_limit);
}
if(parms->skyc.verbose) info2("res0=%g, resmin=%g\n", sqrt(res0)*1e9, sqrt(resmin)*1e9);
dfree(rests);
if(res0<resmin-100e-18){//better by 10 nm
resmin=res0;
kalman_free(kalman_min);
kalman_min=aster->kalman[0];
aster->kalman[0]=0;
idtrat_min=idtrat_limit;
}else{
kalman_free(aster->kalman[0]);aster->kalman[0]=0;
if(isfinite(resmin) && res0>resmin*2){//stop trying.
break;
}
}
}
setup_aster_kalman_dtrat(aster, star, parms, idtrat_min);
if(parms->skyc.verbose) info2("selected\n");
aster->res_ngs->p[0]=resmin;
aster->kalman[0]=kalman_min;
}else{
if(aster->neam) dcellfreearr(aster->neam, ndtrat);
aster->neam=calloc(ndtrat, sizeof(dcell*));
aster->res_ngs=dnew(ndtrat,3);
PDMAT(aster->res_ngs, pres_ngs);
aster->kalman=calloc(ndtrat, sizeof(kalman_t*));
dmat *dtrats=dnew(aster->nwfs,1);
for(int idtrat=0; idtrat<ndtrat; idtrat++){
//assemble neam
//TIC;tic;
aster->neam[idtrat]=cellnew(aster->nwfs, aster->nwfs);
for(int iwfs=0; iwfs<aster->nwfs; iwfs++){
dmat *tmp=ddup(aster->wfs[iwfs].pistat->sanea->p[idtrat]);/*in rad */
dcwpow(tmp, 2);
dsp *tmp2=dspnewdiag(tmp->nx, tmp->p, 1);
dspfull(&aster->neam[idtrat]->p[iwfs+aster->nwfs*iwfs], tmp2,'n',1);
dfree(tmp); dspfree(tmp2);
}
int dtrat=parms->skyc.dtrats->p[idtrat];
for(int iwfs=0; iwfs<aster->nwfs; iwfs++){
dtrats->p[iwfs]=dtrat;
}
aster->kalman[idtrat]=sde_kalman(simu->sdecoeff, parms->maos.dt, dtrats, aster->g, aster->neam[idtrat], 0);
//toc("kalman");
#if 1
dmat *res=skysim_sim(0, simu->mideal, simu->mideal_oa, simu->rmsol, aster, 0, parms, idtrat, 1, -1);
double rms=res?res->p[0]:simu->rmsol;
dfree(res);
#else
dmat *res=kalman_test(aster->kalman[idtrat], simu->mideal);
double rms=calc_rms(res, parms->maos.mcc, parms->skyc.evlstart);
dfree(res);
#endif
//toc("estimate");
pres_ngs[0][idtrat]=rms;
}
dfree(dtrats);
}
}
int gmx_rmsdist(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the root mean square deviation of atom distances,",
"which has the advantage that no fit is needed like in standard RMS",
"deviation as computed by [gmx-rms].",
"The reference structure is taken from the structure file.",
"The RMSD at time t is calculated as the RMS",
"of the differences in distance between atom-pairs in the reference",
"structure and the structure at time t.[PAR]",
"[THISMODULE] can also produce matrices of the rms distances, rms distances",
"scaled with the mean distance and the mean distances and matrices with",
"NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists",
"of atom pairs with 1/r^3 and 1/r^6 averaged distance below the",
"maximum distance ([TT]-max[tt], which will default to 0.6 in this case)",
"can be generated, by default averaging over equivalent hydrogens",
"(all triplets of hydrogens named \\*[123]). Additionally a list of",
"equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
"a set of equivalent atoms specified as residue number and name and",
"atom name; e.g.:[PAR]",
"[TT]HB* 3 SER HB1 3 SER HB2[tt][PAR]",
"Residue and atom names must exactly match those in the structure",
"file, including case. Specifying non-sequential atoms is undefined."
};
int i, teller;
real t;
t_topology top;
int ePBC;
t_atoms *atoms;
matrix box;
rvec *x;
FILE *fp;
t_trxstatus *status;
int isize, gnr = 0;
atom_id *index, *noe_index;
char *grpname;
real **d_r, **d, **dtot, **dtot2, **mean, **rms, **rmsc, *resnr;
real **dtot1_3 = NULL, **dtot1_6 = NULL;
real rmsnow, meanmax, rmsmax, rmscmax;
real max1_3, max1_6;
t_noe_gr *noe_gr = NULL;
t_noe **noe = NULL;
t_rgb rlo, rhi;
gmx_bool bRMS, bScale, bMean, bNOE, bNMR3, bNMR6, bNMR;
static int nlevels = 40;
static real scalemax = -1.0;
static gmx_bool bSumH = TRUE;
static gmx_bool bPBC = TRUE;
output_env_t oenv;
t_pargs pa[] = {
{ "-nlevels", FALSE, etINT, {&nlevels},
"Discretize RMS in this number of levels" },
{ "-max", FALSE, etREAL, {&scalemax},
"Maximum level in matrices" },
{ "-sumh", FALSE, etBOOL, {&bSumH},
"Average distance over equivalent hydrogens" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions when computing distances" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-equiv", "equiv", ffOPTRD },
{ efXVG, NULL, "distrmsd", ffWRITE },
{ efXPM, "-rms", "rmsdist", ffOPTWR },
{ efXPM, "-scl", "rmsscale", ffOPTWR },
{ efXPM, "-mean", "rmsmean", ffOPTWR },
{ efXPM, "-nmr3", "nmr3", ffOPTWR },
{ efXPM, "-nmr6", "nmr6", ffOPTWR },
{ efDAT, "-noe", "noe", ffOPTWR },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bRMS = opt2bSet("-rms", NFILE, fnm);
bScale = opt2bSet("-scl", NFILE, fnm);
bMean = opt2bSet("-mean", NFILE, fnm);
bNOE = opt2bSet("-noe", NFILE, fnm);
bNMR3 = opt2bSet("-nmr3", NFILE, fnm);
bNMR6 = opt2bSet("-nmr6", NFILE, fnm);
bNMR = bNMR3 || bNMR6 || bNOE;
max1_3 = 0;
max1_6 = 0;
/* check input */
if (bNOE && scalemax < 0)
{
scalemax = 0.6;
fprintf(stderr, "WARNING: using -noe without -max "
"makes no sense, setting -max to %g\n\n", scalemax);
}
/* get topology and index */
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, FALSE);
if (!bPBC)
{
ePBC = epbcNONE;
}
atoms = &(top.atoms);
get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* initialize arrays */
snew(d, isize);
snew(dtot, isize);
snew(dtot2, isize);
if (bNMR)
{
snew(dtot1_3, isize);
snew(dtot1_6, isize);
}
snew(mean, isize);
snew(rms, isize);
snew(rmsc, isize);
snew(d_r, isize);
snew(resnr, isize);
for (i = 0; (i < isize); i++)
{
snew(d[i], isize);
snew(dtot[i], isize);
snew(dtot2[i], isize);
if (bNMR)
{
snew(dtot1_3[i], isize);
snew(dtot1_6[i], isize);
}
snew(mean[i], isize);
snew(rms[i], isize);
snew(rmsc[i], isize);
snew(d_r[i], isize);
resnr[i] = i+1;
}
/*set box type*/
calc_dist(isize, index, x, ePBC, box, d_r);
sfree(x);
/*open output files*/
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS Deviation", "Time (ps)", "RMSD (nm)",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"of distances between %s atoms\"\n", grpname);
}
/*do a first step*/
read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
teller = 0;
do
{
calc_dist_tot(isize, index, x, ePBC, box, d, dtot, dtot2, bNMR, dtot1_3, dtot1_6);
rmsnow = rms_diff(isize, d, d_r);
fprintf(fp, "%g %g\n", t, rmsnow);
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
xvgrclose(fp);
close_trj(status);
calc_rms(isize, teller, dtot, dtot2, rms, &rmsmax, rmsc, &rmscmax, mean, &meanmax);
fprintf(stderr, "rmsmax = %g, rmscmax = %g\n", rmsmax, rmscmax);
if (bNMR)
{
calc_nmr(isize, teller, dtot1_3, dtot1_6, &max1_3, &max1_6);
}
if (scalemax > -1.0)
{
rmsmax = scalemax;
rmscmax = scalemax;
meanmax = scalemax;
max1_3 = scalemax;
max1_6 = scalemax;
}
if (bNOE)
{
/* make list of noe atom groups */
snew(noe_index, isize+1);
snew(noe_gr, isize);
gnr = analyze_noe_equivalent(opt2fn_null("-equiv", NFILE, fnm),
atoms, isize, index, bSumH, noe_index, noe_gr);
fprintf(stdout, "Found %d non-equivalent atom-groups in %d atoms\n",
gnr, isize);
/* make half matrix of of noe-group distances from atom distances */
snew(noe, gnr);
for (i = 0; i < gnr; i++)
{
snew(noe[i], gnr);
}
calc_noe(isize, noe_index, dtot1_3, dtot1_6, gnr, noe);
}
rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
if (bRMS)
{
write_xpm(opt2FILE("-rms", NFILE, fnm, "w"), 0,
"RMS of distance", "RMS (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, rms, 0.0, rmsmax, rlo, rhi, &nlevels);
}
if (bScale)
{
write_xpm(opt2FILE("-scl", NFILE, fnm, "w"), 0,
"Relative RMS", "RMS", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, rmsc, 0.0, rmscmax, rlo, rhi, &nlevels);
}
if (bMean)
{
write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0,
"Mean Distance", "Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, mean, 0.0, meanmax, rlo, rhi, &nlevels);
}
if (bNMR3)
{
write_xpm(opt2FILE("-nmr3", NFILE, fnm, "w"), 0, "1/r^3 averaged distances",
"Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, dtot1_3, 0.0, max1_3, rlo, rhi, &nlevels);
}
if (bNMR6)
{
write_xpm(opt2FILE("-nmr6", NFILE, fnm, "w"), 0, "1/r^6 averaged distances",
"Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, dtot1_6, 0.0, max1_6, rlo, rhi, &nlevels);
}
if (bNOE)
{
write_noe(opt2FILE("-noe", NFILE, fnm, "w"), gnr, noe, noe_gr, scalemax);
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
return 0;
}
