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35 /* The make_edi program was generously contributed by Oliver Lange, based
36 * on the code from g_anaeig. You can reach him as olange@gwdg.de. He
37 * probably also holds copyright to the following code.
46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/fileio/pdbio.h"
49 #include "gromacs/fileio/xvgr.h"
50 #include "gromacs/gmxana/eigio.h"
51 #include "gromacs/gmxana/gmx_ana.h"
52 #include "gromacs/math/functions.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/topology/index.h"
55 #include "gromacs/topology/topology.h"
56 #include "gromacs/utility/arraysize.h"
57 #include "gromacs/utility/cstringutil.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/futil.h"
60 #include "gromacs/utility/smalloc.h"
66 gmx_bool bConstForce; /* Do constant force flooding instead of
67 evaluating a flooding potential */
76 /* This type is for the average, reference, target, and origin structure */
79 int nr; /* number of atoms this structure contains */
80 int *anrs; /* atom index numbers */
81 rvec *x; /* positions */
82 real *sqrtm; /* sqrt of the masses used for mass-
83 * weighting of analysis */
89 int nini; /* total Nr of atoms */
90 gmx_bool fitmas; /* true if trans fit with cm */
91 gmx_bool pcamas; /* true if mass-weighted PCA */
92 int presteps; /* number of steps to run without any
93 * perturbations ... just monitoring */
94 int outfrq; /* freq (in steps) of writing to edo */
95 int maxedsteps; /* max nr of steps per cycle */
96 struct edix sref; /* reference positions, to these fitting
98 struct edix sav; /* average positions */
99 struct edix star; /* target positions */
100 struct edix sori; /* origin positions */
101 real slope; /* minimal slope in acceptance radexp */
102 int ned; /* Nr of atoms in essdyn buffer */
103 t_edflood flood; /* parameters especially for flooding */
108 static void make_t_edx(struct edix *edx, int natoms, rvec *pos, int index[])
115 static void write_t_edx(FILE *fp, struct edix edx, const char *comment)
117 /*here we copy only the pointers into the t_edx struct
118 no data is copied and edx.box is ignored */
120 fprintf(fp, "#%s \n %d \n", comment, edx.nr);
121 for (i = 0; i < edx.nr; i++)
123 fprintf(fp, "%d %f %f %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
127 static int sscan_list(int *list[], const char *str, const char *listname)
129 /*this routine scans a string of the form 1,3-6,9 and returns the
130 selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
131 memory for this list will be allocated in this routine -- sscan_list expects *list to
134 listname is a string used in the errormessage*/
139 char *pos, *startpos, *step;
140 int n = std::strlen(str);
142 /*enums to define the different lexical stati */
144 sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
147 int status = sBefore; /*status of the deterministic automat to scan str */
151 char *start = nullptr; /*holds the string of the number behind a ','*/
152 char *end = nullptr; /*holds the string of the number behind a '-' */
154 int nvecs = 0; /* counts the number of vectors in the list*/
159 std::strcpy(pos, str);
166 while ((c = *pos) != 0)
170 /* expect a number */
184 /* have read a number, expect ',' or '-' */
189 srenew(*list, nvecs+1);
190 (*list)[nvecs++] = number = std::strtol(start, nullptr, 10);
200 status = sMinus; break;
202 else if (std::isdigit(c))
212 /* have read a '-' -> expect a number */
217 status = sRange; break;
230 status = sError; break;
245 /* have read the number after a minus, expect ',' or ':' */
250 end_number = std::strtol(end, nullptr, 10);
251 number = std::strtol(start, nullptr, 10);
255 status = sZero; break;
257 if (end_number <= number)
259 status = sSmaller; break;
261 srenew(*list, nvecs+end_number-number+1);
264 istep = strtol(step, nullptr, 10);
271 for (i = number; i <= end_number; i += istep)
273 (*list)[nvecs++] = i;
279 status = sSteppedRange;
282 else if (std::isdigit(c))
292 /* format error occured */
294 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d with char %c", listname, pos-startpos, *(pos-1));
296 /* logical error occured */
298 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid", listname, pos-startpos);
301 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: second index %d is not bigger than %d", listname, pos-startpos, end_number, number);
304 ++pos; /* read next character */
305 } /*scanner has finished */
307 /* append zero to list of eigenvectors */
308 srenew(*list, nvecs+1);
314 static void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
316 /* eig_list is a zero-terminated list of indices into the eigvecs array.
317 eigvecs are coordinates of eigenvectors
318 grouptitle to write in the comment line
319 steps -- array with stepsizes for evLINFIX, evLINACC and evRADACC
322 int n = 0, i; rvec x;
323 while (eig_list[n++])
325 ; /*count selected eigenvecs*/
328 fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);
330 /* write list of eigenvector indicess */
331 for (n = 0; eig_list[n]; n++)
335 fprintf(fp, "%8d %g\n", eig_list[n], steps[n]);
339 fprintf(fp, "%8d %g\n", eig_list[n], 1.0);
344 /* dump coordinates of the selected eigenvectors */
347 for (i = 0; i < natoms; i++)
349 if (eig_list[n] > nvec)
351 gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
353 copy_rvec(eigvecs[eig_list[n]-1][i], x);
354 fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
361 /*enum referring to the different lists of eigenvectors*/
363 evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON, evNr
369 static void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
370 int nvec, int *eig_listen[], real* evStepList[])
375 fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
376 MAGIC, edpars->nini, edpars->fitmas, edpars->pcamas);
377 fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
378 edpars->outfrq, edpars->maxedsteps, edpars->slope);
379 fprintf(fp, "#PRESTEPS\n %d\n#DELTA_F0\n %f\n#INIT_DELTA_F\n %f\n#TAU\n %f\n#EFL_NULL\n %f\n#ALPHA2\n %f\n#KT\n %f\n#HARMONIC\n %d\n#CONST_FORCE_FLOODING\n %d\n",
380 edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
381 edpars->flood.alpha2, edpars->flood.kT, edpars->flood.bHarmonic, edpars->flood.bConstForce);
383 /* Average and reference positions */
384 write_t_edx(fp, edpars->sref, "NREF, XREF");
385 write_t_edx(fp, edpars->sav, "NAV, XAV");
389 write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", nullptr);
390 write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
391 write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
392 write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
393 write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", nullptr);
394 write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", nullptr);
395 write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
398 /*Target and Origin positions */
399 write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
400 write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
403 static int read_conffile(const char *confin, rvec **x)
407 printf("read coordnumber from file %s\n", confin);
408 read_tps_conf(confin, &top, nullptr, x, nullptr, box, FALSE);
409 printf("number of coordinates in file %d\n", top.atoms.nr);
414 static void read_eigenvalues(int vecs[], const char *eigfile, real values[],
415 gmx_bool bHesse, real kT, int natoms_average_struct)
420 neig = read_xvg(eigfile, &eigval, &nrow);
422 fprintf(stderr, "Read %d eigenvalues\n", neig);
423 for (i = bHesse ? 6 : 0; i < neig; i++)
425 if (eigval[1][i] < -0.001 && bHesse)
428 "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
431 if (eigval[1][i] < 0)
438 for (i = 0; vecs[i]; i++)
442 gmx_fatal(FARGS, "ERROR: You have chosen one of the first 6 eigenvectors of the HESSE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
444 values[i] = eigval[1][vecs[i]-1]/kT;
449 for (i = 0; vecs[i]; i++)
451 /* Make sure this eigenvalue does not correspond to one of the last 6 eigenvectors of the
452 * covariance matrix. These correspond to the rotational and translational degrees of
453 * freedom and will be zero within numerical accuracy.
455 * Note that the total number of eigenvectors produced by gmx covar depends on:
456 * 1) the total number of degrees of freedom of the system (3N, with N the number of atoms)
457 * 2) the number S of independent configurations fed into gmx covar.
458 * For long trajectories with lots of frames, usually S >= 3N + 1, so that one indeed gets
459 * 3N eigenvalues (of which the last 6 will have zero eigenvalues).
460 * For S < 3N + 1, however, the covariance matrix becomes rank deficient, and the number
461 * of possible eigenvalues is just S - 1. Since in make_edi we only know N but not S, we can
462 * only warn the user if he picked one of the last 6 of 3N.
464 if (vecs[i] > ( 3 * natoms_average_struct - 6 ))
466 gmx_fatal(FARGS, "ERROR: You have chosen one of the last 6 eigenvectors of the COVARIANCE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
468 values[i] = 1/eigval[1][vecs[i]-1];
472 for (i = 0; i < nrow; i++)
480 static real *scan_vecparams(const char *str, const char * par, int nvecs)
482 char f0[256], f1[256]; /*format strings adapted every pass of the loop*/
487 snew(vec_params, nvecs);
491 for (i = 0; (i < nvecs); i++)
493 std::strcpy(f1, f0); /*f0 is the format string for the "to-be-ignored" numbers*/
494 std::strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
495 if (sscanf(str, f1, &d) != 1)
497 gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
500 std::strcat(f0, "%*s");
507 static void init_edx(struct edix *edx)
514 static void filter2edx(struct edix *edx, int nindex, int index[], int ngro,
515 int igro[], const rvec *x, const char* structure)
517 /* filter2edx copies coordinates from x to edx which are given in index
523 srenew(edx->x, edx->nr);
524 srenew(edx->anrs, edx->nr);
525 for (i = 0; i < nindex; i++, ix++)
527 for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
530 ; /*search element in igro*/
531 if (igro[pos] != index[i])
533 gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
535 edx->anrs[ix] = index[i];
536 copy_rvec(x[pos], edx->x[ix]);
540 static void get_structure(const t_atoms *atoms, const char *IndexFile,
541 const char *StructureFile, struct edix *edx, int nfit,
542 int ifit[], int nav, int index[])
544 int *igro; /*index corresponding to target or origin structure*/
551 ntar = read_conffile(StructureFile, &xtar);
552 printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
553 ntar, StructureFile);
554 get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
557 gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
560 filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
562 /* If average and reference/fitting structure differ, append the average structure as well */
563 if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
565 filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
569 int gmx_make_edi(int argc, char *argv[])
572 static const char *desc[] = {
573 "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
574 "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
575 "normal modes analysis ([gmx-nmeig]).",
576 "ED sampling can be used to manipulate the position along collective coordinates",
577 "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
578 "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
579 "the system to explore new regions along these collective coordinates. A number",
580 "of different algorithms are implemented to drive the system along the eigenvectors",
581 "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
582 "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
583 "or to only monitor the projections of the positions onto",
584 "these coordinates ([TT]-mon[tt]).[PAR]",
586 "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
587 "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
588 "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[PAR]",
589 "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
590 "Towards an exhaustive sampling of the configurational spaces of the ",
591 "two forms of the peptide hormone guanylin,",
592 "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[PAR]",
593 "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
594 "An extended sampling of the configurational space of HPr from E. coli",
595 "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
596 "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
597 "reference structure, target positions, etc.[PAR]",
599 "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
600 "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
601 "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
602 "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
603 "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
604 "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
605 "(steps in the desired direction will be accepted, others will be rejected).",
606 "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
607 "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
608 "to read in a structure file that defines an external origin.[PAR]",
609 "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
610 "towards a target structure specified with [TT]-tar[tt].[PAR]",
611 "NOTE: each eigenvector can be selected only once. [PAR]",
612 "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [REF].xvg[ref] file[PAR]",
613 "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
614 "cycle will be started if the spontaneous increase of the radius (in nm/step)",
615 "is less than the value specified.[PAR]",
616 "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
617 "before a new cycle is started.[PAR]",
618 "Note on the parallel implementation: since ED sampling is a 'global' thing",
619 "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
620 "is not very parallel-friendly from an implementation point of view. Because",
621 "parallel ED requires some extra communication, expect the performance to be",
622 "lower as in a free MD simulation, especially on a large number of ranks and/or",
623 "when the ED group contains a lot of atoms. [PAR]",
624 "Please also note that if your ED group contains more than a single protein,",
625 "then the [REF].tpr[ref] file must contain the correct PBC representation of the ED group.",
626 "Take a look on the initial RMSD from the reference structure, which is printed",
627 "out at the start of the simulation; if this is much higher than expected, one",
628 "of the ED molecules might be shifted by a box vector. [PAR]",
629 "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [REF].xvg[ref] file",
630 "as a function of time in intervals of OUTFRQ steps.[PAR]",
631 "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
632 "a single simulation (on different molecules) if several [REF].edi[ref] files were concatenated",
633 "first. The constraints are applied in the order they appear in the [REF].edi[ref] file. ",
634 "Depending on what was specified in the [REF].edi[ref] input file, the output file contains for each ED dataset",
636 " * the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)",
637 " * projections of the positions onto selected eigenvectors",
640 "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
641 "which will lead to extra forces expelling the structure out of the region described",
642 "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
643 "is kept in that region.",
645 "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
646 "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
647 "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
648 "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
649 "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
650 "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
651 "To use constant Efl set [TT]-tau[tt] to zero.",
653 "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
654 "to give good results for most standard cases in flooding of proteins.",
655 "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
656 "increase, this is mimicked by [GRK]alpha[grk] > 1.",
657 "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
659 "RESTART and FLOODING:",
660 "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
661 "the output file and manually put them into the [REF].edi[ref] file under DELTA_F0 and EFL_NULL."
664 /* Save all the params in this struct and then save it in an edi file.
665 * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
667 static t_edipar edi_params;
670 evStepNr = evRADFIX + 1
672 static const char* evSelections[evNr] = {nullptr, nullptr, nullptr, nullptr, nullptr, nullptr};
673 static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
674 static const char* evParams[evStepNr] = {nullptr, nullptr};
675 static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
676 static const char* ConstForceStr;
677 static real * evStepList[evStepNr];
678 static real radstep = 0.0;
679 static real deltaF0 = 150;
680 static real deltaF = 0;
681 static real tau = .1;
682 static real constEfl = 0.0;
683 static real alpha = 1;
684 static int eqSteps = 0;
685 static int * listen[evNr];
686 static real T = 300.0;
687 const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
688 static gmx_bool bRestrain = FALSE;
689 static gmx_bool bHesse = FALSE;
690 static gmx_bool bHarmonic = FALSE;
692 { "-mon", FALSE, etSTR, {&evSelections[evMON]},
693 "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
694 { "-linfix", FALSE, etSTR, {&evSelections[0]},
695 "Indices of eigenvectors for fixed increment linear sampling" },
696 { "-linacc", FALSE, etSTR, {&evSelections[1]},
697 "Indices of eigenvectors for acceptance linear sampling" },
698 { "-radfix", FALSE, etSTR, {&evSelections[3]},
699 "Indices of eigenvectors for fixed increment radius expansion" },
700 { "-radacc", FALSE, etSTR, {&evSelections[4]},
701 "Indices of eigenvectors for acceptance radius expansion" },
702 { "-radcon", FALSE, etSTR, {&evSelections[5]},
703 "Indices of eigenvectors for acceptance radius contraction" },
704 { "-flood", FALSE, etSTR, {&evSelections[2]},
705 "Indices of eigenvectors for flooding"},
706 { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
707 "Frequency (in steps) of writing output in [REF].xvg[ref] file" },
708 { "-slope", FALSE, etREAL, { &edi_params.slope},
709 "Minimal slope in acceptance radius expansion"},
710 { "-linstep", FALSE, etSTR, {&evParams[0]},
711 "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
712 { "-accdir", FALSE, etSTR, {&evParams[1]},
713 "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
714 { "-radstep", FALSE, etREAL, {&radstep},
715 "Stepsize (nm/step) for fixed increment radius expansion"},
716 { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
717 "Maximum number of steps per cycle" },
718 { "-eqsteps", FALSE, etINT, {&eqSteps},
719 "Number of steps to run without any perturbations "},
720 { "-deltaF0", FALSE, etREAL, {&deltaF0},
721 "Target destabilization energy for flooding"},
722 { "-deltaF", FALSE, etREAL, {&deltaF},
723 "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
724 { "-tau", FALSE, etREAL, {&tau},
725 "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
726 { "-Eflnull", FALSE, etREAL, {&constEfl},
727 "The starting value of the flooding strength. The flooding strength is updated "
728 "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
729 { "-T", FALSE, etREAL, {&T},
730 "T is temperature, the value is needed if you want to do flooding "},
731 { "-alpha", FALSE, etREAL, {&alpha},
732 "Scale width of gaussian flooding potential with alpha^2 "},
733 { "-restrain", FALSE, etBOOL, {&bRestrain},
734 "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
735 { "-hessian", FALSE, etBOOL, {&bHesse},
736 "The eigenvectors and eigenvalues are from a Hessian matrix"},
737 { "-harmonic", FALSE, etBOOL, {&bHarmonic},
738 "The eigenvalues are interpreted as spring constant"},
739 { "-constF", FALSE, etSTR, {&ConstForceStr},
740 "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
741 "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
743 #define NPA asize(pa)
746 int nvec1, *eignr1 = nullptr;
747 rvec *xav1, **eigvec1 = nullptr;
748 t_atoms *atoms = nullptr;
749 int nav; /* Number of atoms in the average structure */
751 const char *indexfile;
754 int nfit; /* Number of atoms in the reference/fit structure */
755 int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
757 real *eigval1 = nullptr; /* in V3.3 this is parameter of read_eigenvectors */
760 const char *TargetFile;
761 const char *OriginFile;
762 const char *EigvecFile;
764 gmx_output_env_t *oenv;
766 /*to read topology file*/
774 { efTRN, "-f", "eigenvec", ffREAD },
775 { efXVG, "-eig", "eigenval", ffOPTRD },
776 { efTPS, nullptr, nullptr, ffREAD },
777 { efNDX, nullptr, nullptr, ffOPTRD },
778 { efSTX, "-tar", "target", ffOPTRD},
779 { efSTX, "-ori", "origin", ffOPTRD},
780 { efEDI, "-o", "sam", ffWRITE }
782 #define NFILE asize(fnm)
783 edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
784 if (!parse_common_args(&argc, argv, 0,
785 NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
790 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
791 EdiFile = ftp2fn(efEDI, NFILE, fnm);
792 TargetFile = opt2fn_null("-tar", NFILE, fnm);
793 OriginFile = opt2fn_null("-ori", NFILE, fnm);
796 for (ev_class = 0; ev_class < evNr; ++ev_class)
798 if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
800 /*get list of eigenvectors*/
801 nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
802 if (ev_class < evStepNr-2)
804 /*if apropriate get list of stepsizes for these eigenvectors*/
805 if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
807 evStepList[ev_class] =
808 scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
810 else /*if list is not given fill with zeros */
812 snew(evStepList[ev_class], nvecs);
813 for (i = 0; i < nvecs; i++)
815 evStepList[ev_class][i] = 0.0;
819 else if (ev_class == evRADFIX)
821 snew(evStepList[ev_class], nvecs);
822 for (i = 0; i < nvecs; i++)
824 evStepList[ev_class][i] = radstep;
827 else if (ev_class == evFLOOD)
829 snew(evStepList[ev_class], nvecs);
831 /* Are we doing constant force flooding? In that case, we read in
832 * the fproj values from the command line */
833 if (opt2parg_bSet("-constF", NPA, pa))
835 evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
840 }; /*to avoid ambiguity */
842 else /* if there are no eigenvectors for this option set list to zero */
844 listen[ev_class] = nullptr;
845 snew(listen[ev_class], 1);
846 listen[ev_class][0] = 0;
850 /* print the interpreted list of eigenvectors - to give some feedback*/
851 for (ev_class = 0; ev_class < evNr; ++ev_class)
853 printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
855 while (listen[ev_class][i])
857 printf("%d ", listen[ev_class][i++]);
862 EigvecFile = opt2fn("-f", NFILE, fnm);
864 /*read eigenvectors from eigvec.trr*/
865 read_eigenvectors(EigvecFile, &nav, &bFit1,
866 &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
868 read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
869 &top, &ePBC, &xtop, nullptr, topbox, 0);
873 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
874 get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
877 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
883 if (xref1 == nullptr)
887 /* if g_covar used different coordinate groups to fit and to do the PCA */
888 printf("\nNote: the structure in %s should be the same\n"
889 " as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
890 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
894 printf("\nNote: Apparently no fitting was done in g_covar.\n"
895 " However, you need to select a reference group for fitting in mdrun\n");
897 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
899 for (i = 0; i < nfit; i++)
901 copy_rvec(xtop[ifit[i]], xref1[i]);
910 if (opt2parg_bSet("-constF", NPA, pa))
912 /* Constant force flooding is special: Most of the normal flooding
913 * options are not needed. */
914 edi_params.flood.bConstForce = TRUE;
918 /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
920 if (listen[evFLOOD][0] != 0)
922 read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T, nav);
925 edi_params.flood.tau = tau;
926 edi_params.flood.deltaF0 = deltaF0;
927 edi_params.flood.deltaF = deltaF;
928 edi_params.presteps = eqSteps;
929 edi_params.flood.kT = kB*T;
930 edi_params.flood.bHarmonic = bHarmonic;
933 /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
934 edi_params.flood.constEfl = -constEfl;
935 edi_params.flood.alpha2 = -gmx::square(alpha);
939 edi_params.flood.constEfl = constEfl;
940 edi_params.flood.alpha2 = gmx::square(alpha);
944 edi_params.ned = nav;
946 /*number of system atoms */
947 edi_params.nini = atoms->nr;
950 /*store reference and average structure in edi_params*/
951 make_t_edx(&edi_params.sref, nfit, xref1, ifit );
952 make_t_edx(&edi_params.sav, nav, xav1, index);
955 /* Store target positions in edi_params */
956 if (opt2bSet("-tar", NFILE, fnm))
958 if (0 != listen[evFLOOD][0])
960 fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
961 " You may want to use -ori to define the flooding potential center.\n\n");
963 get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
967 make_t_edx(&edi_params.star, 0, nullptr, index);
970 /* Store origin positions */
971 if (opt2bSet("-ori", NFILE, fnm))
973 get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
977 make_t_edx(&edi_params.sori, 0, nullptr, index);
981 write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);