Lines Matching refs:_opt
46 treekin_options *_opt; variable
262 _opt = &globalParameters->opt; in Calc()
265 _kT = 0.00198717 * (273.15 + _opt->T); in Calc()
273 solver = new Calccpp(_opt, _E); in Calc()
367 if (!_opt->quiet) in MxEgro()
388 PrintProb(line, 1, _opt->t0); in PrintDummy()
389 PrintProb(line, 1, _opt->t8); in PrintDummy()
419 if (_opt->num_err == 'H') in PrintProbFull()
421 else if (_opt->num_err == 'R') in PrintProbFull()
432 (_opt->num_err == 'R' ? "rescaling" : "exiting")); in PrintProbFull()
433 if (_opt->num_err == 'H' || check == 0.0) in PrintProbFull()
440 if (_opt->num_err == 'R') in PrintProbFull()
464 if (_opt->num_err == 'H') in PrintProbNR()
466 else if (_opt->num_err == 'R') in PrintProbNR()
477 (_opt->num_err == 'R' ? "rescaling" : "exiting")); in PrintProbNR()
478 if (_opt->num_err == 'H' || check == 0.0) in PrintProbNR()
485 if (_opt->num_err == 'R') in PrintProbNR()
513 if (_opt->num_err == 'H') in PrintProb()
515 else if (_opt->num_err == 'R') in PrintProb()
525 (_opt->num_err == 'R' && (double)check != 0.0 ? "rescaling" : "exiting")); in PrintProb()
526 if (_opt->num_err == 'H' || check == 0.0) in PrintProb()
535 if (_opt->num_err == 'R') in PrintProb()
546 if (_opt->num_err == 'R') in PrintProb()
612 if (_opt->want_degenerate) in MxBar2Matrix()
615 switch (_opt->method) { in MxBar2Matrix()
629 "ERROR in MxBar2Matrix(): No handler 4 method %c\n", _opt->method); in MxBar2Matrix()
632 if (_opt->dumpU) { in MxBar2Matrix()
656 if (!_opt->absrb) { in MxGetSpace()
674 if (_opt->pini) { in MxStartVec()
675 for (i = 1; i < (int)*_opt->pini; i += 2) in MxStartVec()
676 pzero[(int)_opt->pini[i] - 1] = (T)_opt->pini[i + 1]; in MxStartVec()
683 if (_opt->want_verbose) in MxStartVec()
700 if (_opt->absrb) { in MxEqDistr()
716 if (_opt->want_verbose) in MxEqDistr()
732 if (_opt->absrb) { in MxEqDistrFULL()
735 p8[_opt->absrb - 1] = 1.; in MxEqDistrFULL()
743 if (_opt->want_verbose) in MxEqDistrFULL()
758 if (_opt->absrb) { in MxEqDistrFromLinSys()
769 if (_opt->want_verbose) in MxEqDistrFromLinSys()
774 … A[n * (i - 1) + (j - 1)] = U[dim * i + j] - (i == j && _opt->useplusI ? 1.0 : 0.0); /*U-I=Q */ in MxEqDistrFromLinSys()
780 if (_opt->want_verbose) in MxEqDistrFromLinSys()
783 if (_opt->want_verbose) in MxEqDistrFromLinSys()
797 if (_opt->want_verbose) in MxEqDistrFromLinSys()
805 if (_opt->want_verbose) in MxEqDistrFromLinSys()
844 if (_opt->want_verbose) in MxEqDistrFromLinSys()
859 if (_opt->dumpMathematica == 1) in MxDiagonalize()
862 if (!_opt->absrb) { in MxDiagonalize()
863 if (_opt->want_verbose) in MxDiagonalize()
870 if (_opt->want_verbose) in MxDiagonalize()
873 if (_opt->want_verbose) in MxDiagonalize()
876 if (_opt->want_verbose) in MxDiagonalize()
882 if (_opt->want_verbose) in MxDiagonalize()
915 if (!_opt->quiet) in MxDiagonalize()
919 if (_opt->want_verbose) in MxDiagonalize()
924 if (_opt->absrb) { in MxDiagonalize()
927 switch (_opt->mlapackMethod) { in MxDiagonalize()
934 _opt->mlapackMethod_Bits); in MxDiagonalize()
945 (mpfr::mpreal *)evecs, _opt->mlapackMethod_Bits); in MxDiagonalize()
979 if (_opt->want_verbose) { in MxDiagonalize()
1000 if (!_opt->quiet) { in MxDiagonalize()
1001 if ((T)abs(evals[0] - ((_opt->useplusI) ? 1. : 0.)) > (T)10 * _opt->FEPS) { in MxDiagonalize()
1011 if (_opt->useplusI) in MxDiagonalize()
1018 if (_opt->useplusI) in MxDiagonalize()
1028 _opt->useplusI ? 1 : 0, in MxDiagonalize()
1031 if (_opt->absrb) in MxDiagonalize()
1038 if (_opt->dumpX) { in MxDiagonalize()
1043 if (_opt->wrecover) { in MxDiagonalize()
1048 if (_opt->want_verbose) { in MxDiagonalize()
1068 if (_opt->useplusI) in MxDiagonalize()
1110 if (_opt->want_verbose) { in MxRecover()
1185 if (_opt->method == 'F') { in MxIterate()
1197 if (!_opt->absrb) { in MxIterate()
1209 if (_opt->want_verbose) { in MxIterate()
1231 mxccm.minv(S_inv, dim, _opt->FEPS); in MxIterate()
1232 if (_opt->want_verbose) in MxIterate()
1239 if (_opt->method == 'F') { in MxIterate()
1247 if (_opt->num_err == 'H' || check == 0.0) { in MxIterate()
1249 } else if (_opt->num_err == 'R') { in MxIterate()
1261 if (_opt->t0 == 0.0) { in MxIterate()
1262 if (_opt->method == 'F') in MxIterate()
1267 _opt->t0 = _globalParameters->TZERO; in MxIterate()
1275 T inc = _opt->t0; in MxIterate()
1276 T t8 = _opt->t8; in MxIterate()
1277 for (tt = inc; tt < _opt->t8 + inc; inc *= _opt->tinc, tt += inc) { in MxIterate()
1278 if (tt > _opt->t8) { in MxIterate()
1279 tt = _opt->t8; in MxIterate()
1286 exptL[dim * i + i] = (T)exp(time / _opt->times * evals[i]); in MxIterate()
1291 underflow[i] = (T)(time / _opt->times); in MxIterate()
1296 if (!_opt->absrb) in MxIterate()
1309 if (_opt->method == 'F') { in MxIterate()
1317 if (_opt->method == 'F') in MxIterate()
1324 if (_opt->method == 'F') in MxIterate()
1335 if (_opt->warnings) { in MxIterate()
1341 if (time < _opt->t8) { in MxIterate()
1342 if (_opt->method == 'F') in MxIterate()
1343 PrintProbFull(pt, dim, _opt->t8, _lmins); in MxIterate()
1345 PrintProb(pt, dim, _opt->t8); in MxIterate()
1352 if (_opt->method == 'F') { in MxIterate()
1407 if (_opt->absrb) { in MxMethodeA()
1412 real_abs = _opt->absrb; /* the original absorbing lmin */ in MxMethodeA()
1414 _opt->absrb = dim; /* the 'new' abs state = last row/column of rate matrix */ in MxMethodeA()
1415 fprintf(stderr, "new absorbing lmin is: %i\n", _opt->absrb); in MxMethodeA()
1430 if (_opt->want_verbose) in MxMethodeA()
1443 if (_opt->useplusI) in MxMethodeA()
1446 if (_opt->want_verbose) in MxMethodeA()
1463 if (_opt->absrb) /*==== absorbing states ====*/
1465 R[dim * i + (_opt->absrb - 1)] = 0.;
1478 if (_opt->useplusI)
1482 if (_opt->want_verbose)
1500 if (_opt->want_verbose) in MxMethodeINPUT()
1503 if (_opt->absrb) { in MxMethodeINPUT()
1508 _opt->real_abs = _opt->absrb; /* the original absorbing lmin */ in MxMethodeINPUT()
1509 _opt->real_abs--; in MxMethodeINPUT()
1510 _opt->absrb = dim; /* the 'new' abs state = last row/column of rate matrix */ in MxMethodeINPUT()
1511 fprintf(stderr, "new absorbing lmin is: %i\n", _opt->absrb); in MxMethodeINPUT()
1512 Zabs = exp((-Data[_opt->real_abs].FGr) / _kT); in MxMethodeINPUT()
1513 abs_rate = (T)(exp((-Data[_opt->real_abs].energy) / _kT) / Zabs); in MxMethodeINPUT()
1523 U[dim * (dim - 1) + _opt->real_abs] = abs_rate; in MxMethodeINPUT()
1543 if (_opt->useplusI) in MxMethodeINPUT()
1555 if (_opt->want_verbose) in MxMethodeINPUT()
1734 if (_opt->want_verbose) { in MxFixevecsAbsorb()
1743 if (_opt->want_verbose) { in MxFixevecsAbsorb()
1750 if (_opt->want_verbose) { in MxFixevecsAbsorb()
1761 if (_opt->absrb && (abscount > 1)) { in MxFixevecsAbsorb()
1763 if (!_opt->quiet) in MxFixevecsAbsorb()
1809 if (_opt->want_verbose) in MxFixevecs()
1857 if (_opt->want_verbose) in MxFixevecs()
1909 if (_opt->basename == NULL) in MxBinWrite()
1912 len = strlen(_opt->basename) + strlen(wosis) + strlen(suffix) + 4; in MxBinWrite()
1916 if (_opt->basename != NULL) { in MxBinWrite()
1917 strcpy(binfile, _opt->basename); in MxBinWrite()
1929 if (!_opt->quiet) in MxBinWrite()
1982 if (_opt->basename == NULL) in MxBinRead()
1985 len = strlen(_opt->basename) + strlen(wosis) + strlen(suffix) + 4; in MxBinRead()
1989 if (_opt->basename != NULL) { in MxBinRead()
1990 strcpy(binfile, _opt->basename); in MxBinRead()
2063 if (!_opt->quiet) in MxASCIIWrite()
2087 if (!_opt->quiet) in MxASCIIWriteV()
2116 if (_opt->t0 == 0.0) { in MxExponent()
2117 if (_opt->method == 'F') in MxExponent()
2122 _opt->t0 = _globalParameters->TZERO; in MxExponent()
2128 for (tt = _opt->t0; tt < _opt->t8 * _opt->tinc; tt *= _opt->tinc) { in MxExponent()
2129 time = (tt < _opt->t8) ? tt : (T)_opt->t8; in MxExponent()
2134 em.padexp(U, Uexp, dim, 30, _opt->FEPS); in MxExponent()
2172 (_opt->num_err == 'R' ? "rescaling" : "exiting")); in MxExponent()
2173 if (_opt->num_err == 'H') { in MxExponent()
2214 if (_opt->absrb) { in MxFPT()
2225 …Z[(dim - 1) * i + j] = (T)((i == j && _opt->useplusI ? 1.0 : 0.0) - U[dim * i + j]); /* I-U = -Q … in MxFPT()
2237 B[i] -= B[_opt->real_abs]; in MxFPT()
2251 …Z[dim * i + j] = (T)((i == j && _opt->useplusI ? 1.0 : 0.0) - U[dim * j + i] + p8[j]); /* I-U+W = … in MxFPT()
2255 mxccm.minv(Z, dim, _opt->FEPS); in MxFPT()
2330 A[n * i + j] = (T)(U[dim * ui + uj] - (i == j && _opt->useplusI ? 1.0 : 0.0)); in MxFPTOneState()
2414 if (!_opt->absrb) { in MxFPTRnd()
2482 abstol = _opt->FEPS; in MxEVLapackSym()
2484 if (_opt->want_verbose) in MxEVLapackSym()
2588 if ((evals_re[i] != 0.0) && abs(evals_im[i] / evals_re[i]) > _opt->FEPS) in MxEVLapackNonSym()
2694 if (_opt->sequence) in MxMemoryCleanUp()
2695 free(_opt->sequence); in MxMemoryCleanUp()
2697 if (_opt->basename) in MxMemoryCleanUp()
2698 free(_opt->basename); in MxMemoryCleanUp()
2700 if (_opt->fpt_file) in MxMemoryCleanUp()
2701 free(_opt->fpt_file); in MxMemoryCleanUp()
2723 _opt->sequence, in print_settings()
2724 _opt->method, in print_settings()
2725 _opt->t0, in print_settings()
2726 _opt->t8, in print_settings()
2727 _opt->T in print_settings()
2729 if (_opt->basename != NULL) in print_settings()
2730 printf("# Basename: %s\n", _opt->basename); in print_settings()
2734 if (_opt->tinc) in print_settings()
2735 printf("# Time increment: %.2f\n", _opt->tinc); in print_settings()
2737 printf("# Time increment: %.2f \n", _opt->tinc); in print_settings()
2739 if (_opt->want_degenerate == 1) in print_settings()
2744 if (_opt->absrb < 1) in print_settings()
2747 printf("# Absorbing state: %d\n", _opt->absrb); in print_settings()
2749 if (_opt->n > 0) in print_settings()
2750 printf("# States limit: %d\n", _opt->n); in print_settings()
2822 if (_opt->want_verbose) { in MxDoDegeneracyStuff()