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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.
48 #include "gromacs/commandline/pargs.h"
51 #include "gromacs/utility/smalloc.h"
53 #include "gmx_fatal.h"
56 #include "gromacs/fileio/futil.h"
57 #include "gromacs/fileio/pdbio.h"
58 #include "gromacs/fileio/confio.h"
59 #include "gromacs/fileio/tpxio.h"
60 #include "gromacs/fileio/matio.h"
67 #include "gromacs/utility/cstringutil.h"
73 gmx_bool bConstForce; /* Do constant force flooding instead of
74 evaluating a flooding potential */
83 /* This type is for the average, reference, target, and origin structure */
86 int nr; /* number of atoms this structure contains */
87 int *anrs; /* atom index numbers */
88 rvec *x; /* positions */
89 real *sqrtm; /* sqrt of the masses used for mass-
90 * weighting of analysis */
96 int nini; /* total Nr of atoms */
97 gmx_bool fitmas; /* true if trans fit with cm */
98 gmx_bool pcamas; /* true if mass-weighted PCA */
99 int presteps; /* number of steps to run without any
100 * perturbations ... just monitoring */
101 int outfrq; /* freq (in steps) of writing to edo */
102 int maxedsteps; /* max nr of steps per cycle */
103 struct edix sref; /* reference positions, to these fitting
105 struct edix sav; /* average positions */
106 struct edix star; /* target positions */
107 struct edix sori; /* origin positions */
108 real slope; /* minimal slope in acceptance radexp */
109 int ned; /* Nr of atoms in essdyn buffer */
110 t_edflood flood; /* parameters especially for flooding */
115 void make_t_edx(struct edix *edx, int natoms, rvec *pos, atom_id index[])
122 void write_t_edx(FILE *fp, struct edix edx, const char *comment)
124 /*here we copy only the pointers into the t_edx struct
125 no data is copied and edx.box is ignored */
127 fprintf(fp, "#%s \n %d \n", comment, edx.nr);
128 for (i = 0; i < edx.nr; i++)
130 fprintf(fp, "%d %f %f %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
134 int sscan_list(int *list[], const char *str, const char *listname)
136 /*this routine scans a string of the form 1,3-6,9 and returns the
137 selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
138 memory for this list will be allocated in this routine -- sscan_list expects *list to
141 listname is a string used in the errormessage*/
146 char *pos, *startpos, *step;
149 /*enums to define the different lexical stati */
151 sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
154 int status = sBefore; /*status of the deterministic automat to scan str */
158 char *start = NULL; /*holds the string of the number behind a ','*/
159 char *end = NULL; /*holds the string of the number behind a '-' */
161 int nvecs = 0; /* counts the number of vectors in the list*/
173 while ((c = *pos) != 0)
177 /* expect a number */
178 case sBefore: if (isdigit(c))
189 /* have read a number, expect ',' or '-' */
190 case sNumber: if (c == ',')
193 srenew(*list, nvecs+1);
194 (*list)[nvecs++] = number = strtol(start, NULL, 10);
204 status = sMinus; break;
215 /* have read a '-' -> expect a number */
220 status = sRange; break;
232 status = sError; break;
246 /* have read the number after a minus, expect ',' or ':' */
251 end_number = strtol(end, NULL, 10);
252 number = strtol(start, NULL, 10);
256 status = sZero; break;
258 if (end_number <= number)
260 status = sSmaller; break;
262 srenew(*list, nvecs+end_number-number+1);
265 istep = strtol(step, NULL, 10);
272 for (i = number; i <= end_number; i += istep)
274 (*list)[nvecs++] = i;
280 status = sSteppedRange;
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 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;
324 while (eig_list[n++])
326 ; /*count selected eigenvecs*/
329 fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);
331 /* write list of eigenvector indicess */
332 for (n = 0; eig_list[n]; n++)
336 fprintf(fp, "%8d %g\n", eig_list[n], steps[n]);
340 fprintf(fp, "%8d %g\n", eig_list[n], 1.0);
345 /* dump coordinates of the selected eigenvectors */
349 for (i = 0; i < natoms; i++)
351 if (eig_list[n] > nvec)
353 gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
355 copy_rvec(eigvecs[eig_list[n]-1][i], x);
357 fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
364 /*enum referring to the different lists of eigenvectors*/
366 evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON, evNr
372 void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
373 int nvec, int *eig_listen[], real* evStepList[])
378 fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
379 MAGIC, edpars->nini, edpars->fitmas, edpars->pcamas);
380 fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
381 edpars->outfrq, edpars->maxedsteps, edpars->slope);
382 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",
383 edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
384 edpars->flood.alpha2, edpars->flood.kT, edpars->flood.bHarmonic, edpars->flood.bConstForce);
386 /* Average and reference positions */
387 write_t_edx(fp, edpars->sref, "NREF, XREF");
388 write_t_edx(fp, edpars->sav, "NAV, XAV");
392 write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", NULL);
393 write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
394 write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
395 write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
396 write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", NULL);
397 write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", NULL);
398 write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
401 /*Target and Origin positions */
402 write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
403 write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
406 int read_conffile(const char *confin, char *title, rvec *x[])
408 /* read coordinates out of STX file */
412 printf("read coordnumber from file %s\n", confin);
413 get_stx_coordnum(confin, &natoms);
414 printf("number of coordinates in file %d\n", natoms);
415 /* if (natoms != ncoords)
416 gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
417 " does not match topology (= %d)",
418 confin,natoms,ncoords);
420 /* make space for coordinates and velocities */
421 init_t_atoms(&confat, natoms, FALSE);
423 read_stx_conf(confin, title, &confat, *x, NULL, NULL, box);
428 void read_eigenvalues(int vecs[], const char *eigfile, real values[],
429 gmx_bool bHesse, real kT)
434 neig = read_xvg(eigfile, &eigval, &nrow);
436 fprintf(stderr, "Read %d eigenvalues\n", neig);
437 for (i = bHesse ? 6 : 0; i < neig; i++)
439 if (eigval[1][i] < -0.001 && bHesse)
442 "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
445 if (eigval[1][i] < 0)
452 for (i = 0; vecs[i]; i++)
456 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");
458 values[i] = eigval[1][vecs[i]-1]/kT;
463 for (i = 0; vecs[i]; i++)
465 if (vecs[i] > (neig-6))
467 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");
469 values[i] = 1/eigval[1][vecs[i]-1];
473 for (i = 0; i < nrow; i++)
481 static real *scan_vecparams(const char *str, const char * par, int nvecs)
483 char f0[256], f1[256]; /*format strings adapted every pass of the loop*/
488 snew(vec_params, nvecs);
492 for (i = 0; (i < nvecs); i++)
494 strcpy(f1, f0); /*f0 is the format string for the "to-be-ignored" numbers*/
495 strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
496 if (sscanf(str, f1, &d) != 1)
498 gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
509 void init_edx(struct edix *edx)
516 void filter2edx(struct edix *edx, int nindex, atom_id index[], int ngro,
517 atom_id igro[], rvec *x, const char* structure)
519 /* filter2edx copies coordinates from x to edx which are given in index
525 srenew(edx->x, edx->nr);
526 srenew(edx->anrs, edx->nr);
527 for (i = 0; i < nindex; i++, ix++)
529 for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
532 ; /*search element in igro*/
533 if (igro[pos] != index[i])
535 gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
537 edx->anrs[ix] = index[i];
538 copy_rvec(x[pos], edx->x[ix]);
542 void get_structure(t_atoms *atoms, const char *IndexFile,
543 const char *StructureFile, struct edix *edx, int nfit,
544 atom_id ifit[], int nav, atom_id index[])
546 atom_id *igro; /*index corresponding to target or origin structure*/
554 ntar = read_conffile(StructureFile, title, &xtar);
555 printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
556 ntar, StructureFile);
557 get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
560 gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
563 filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
565 /* If average and reference/fitting structure differ, append the average structure as well */
566 if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
568 filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
572 int gmx_make_edi(int argc, char *argv[])
575 static const char *desc[] = {
576 "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
577 "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
578 "normal modes analysis ([gmx-nmeig]).",
579 "ED sampling can be used to manipulate the position along collective coordinates",
580 "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
581 "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
582 "the system to explore new regions along these collective coordinates. A number",
583 "of different algorithms are implemented to drive the system along the eigenvectors",
584 "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
585 "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
586 "or to only monitor the projections of the positions onto",
587 "these coordinates ([TT]-mon[tt]).[PAR]",
589 "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
590 "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
591 "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
592 "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
593 "Towards an exhaustive sampling of the configurational spaces of the ",
594 "two forms of the peptide hormone guanylin,",
595 "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
596 "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
597 "An extended sampling of the configurational space of HPr from E. coli",
598 "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
599 "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
600 "reference structure, target positions, etc.[PAR]",
602 "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
603 "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
604 "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
605 "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
606 "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
607 "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
608 "(steps in the desired direction will be accepted, others will be rejected).",
609 "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
610 "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
611 "to read in a structure file that defines an external origin.[PAR]",
612 "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
613 "towards a target structure specified with [TT]-tar[tt].[PAR]",
614 "NOTE: each eigenvector can be selected only once. [PAR]",
615 "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
616 "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
617 "cycle will be started if the spontaneous increase of the radius (in nm/step)",
618 "is less than the value specified.[PAR]",
619 "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
620 "before a new cycle is started.[PAR]",
621 "Note on the parallel implementation: since ED sampling is a 'global' thing",
622 "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
623 "is not very parallel-friendly from an implementation point of view. Because",
624 "parallel ED requires some extra communication, expect the performance to be",
625 "lower as in a free MD simulation, especially on a large number of nodes and/or",
626 "when the ED group contains a lot of atoms. [PAR]",
627 "Please also note that if your ED group contains more than a single protein,",
628 "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
629 "Take a look on the initial RMSD from the reference structure, which is printed",
630 "out at the start of the simulation; if this is much higher than expected, one",
631 "of the ED molecules might be shifted by a box vector. [PAR]",
632 "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
633 "as a function of time in intervals of OUTFRQ steps.[PAR]",
634 "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
635 "a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
636 "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
637 "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
638 "[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
639 "[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
642 "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
643 "which will lead to extra forces expelling the structure out of the region described",
644 "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
645 "is kept in that region.",
647 "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
648 "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
649 "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
650 "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
651 "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
652 "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
653 "To use constant Efl set [TT]-tau[tt] to zero.",
655 "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
656 "to give good results for most standard cases in flooding of proteins.",
657 "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
658 "increase, this is mimicked by [GRK]alpha[grk] > 1.",
659 "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
661 "RESTART and FLOODING:",
662 "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
663 "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
666 /* Save all the params in this struct and then save it in an edi file.
667 * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
669 static t_edipar edi_params;
672 evStepNr = evRADFIX + 1
674 static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
675 static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
676 static const char* evParams[evStepNr] = {NULL, NULL};
677 static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
678 static const char* ConstForceStr;
679 static real * evStepList[evStepNr];
680 static real radstep = 0.0;
681 static real deltaF0 = 150;
682 static real deltaF = 0;
683 static real tau = .1;
684 static real constEfl = 0.0;
685 static real alpha = 1;
686 static int eqSteps = 0;
687 static int * listen[evNr];
688 static real T = 300.0;
689 const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
690 static gmx_bool bRestrain = FALSE;
691 static gmx_bool bHesse = FALSE;
692 static gmx_bool bHarmonic = FALSE;
694 { "-mon", FALSE, etSTR, {&evSelections[evMON]},
695 "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
696 { "-linfix", FALSE, etSTR, {&evSelections[0]},
697 "Indices of eigenvectors for fixed increment linear sampling" },
698 { "-linacc", FALSE, etSTR, {&evSelections[1]},
699 "Indices of eigenvectors for acceptance linear sampling" },
700 { "-radfix", FALSE, etSTR, {&evSelections[3]},
701 "Indices of eigenvectors for fixed increment radius expansion" },
702 { "-radacc", FALSE, etSTR, {&evSelections[4]},
703 "Indices of eigenvectors for acceptance radius expansion" },
704 { "-radcon", FALSE, etSTR, {&evSelections[5]},
705 "Indices of eigenvectors for acceptance radius contraction" },
706 { "-flood", FALSE, etSTR, {&evSelections[2]},
707 "Indices of eigenvectors for flooding"},
708 { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
709 "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
710 { "-slope", FALSE, etREAL, { &edi_params.slope},
711 "Minimal slope in acceptance radius expansion"},
712 { "-linstep", FALSE, etSTR, {&evParams[0]},
713 "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
714 { "-accdir", FALSE, etSTR, {&evParams[1]},
715 "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
716 { "-radstep", FALSE, etREAL, {&radstep},
717 "Stepsize (nm/step) for fixed increment radius expansion"},
718 { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
719 "Maximum number of steps per cycle" },
720 { "-eqsteps", FALSE, etINT, {&eqSteps},
721 "Number of steps to run without any perturbations "},
722 { "-deltaF0", FALSE, etREAL, {&deltaF0},
723 "Target destabilization energy for flooding"},
724 { "-deltaF", FALSE, etREAL, {&deltaF},
725 "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
726 { "-tau", FALSE, etREAL, {&tau},
727 "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
728 { "-Eflnull", FALSE, etREAL, {&constEfl},
729 "The starting value of the flooding strength. The flooding strength is updated "
730 "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
731 { "-T", FALSE, etREAL, {&T},
732 "T is temperature, the value is needed if you want to do flooding "},
733 { "-alpha", FALSE, etREAL, {&alpha},
734 "Scale width of gaussian flooding potential with alpha^2 "},
735 { "-restrain", FALSE, etBOOL, {&bRestrain},
736 "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
737 { "-hessian", FALSE, etBOOL, {&bHesse},
738 "The eigenvectors and eigenvalues are from a Hessian matrix"},
739 { "-harmonic", FALSE, etBOOL, {&bHarmonic},
740 "The eigenvalues are interpreted as spring constant"},
741 { "-constF", FALSE, etSTR, {&ConstForceStr},
742 "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
743 "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
745 #define NPA asize(pa)
748 int nvec1, *eignr1 = NULL;
749 rvec *xav1, **eigvec1 = NULL;
750 t_atoms *atoms = NULL;
751 int nav; /* Number of atoms in the average structure */
753 const char *indexfile;
755 atom_id *index, *ifit;
756 int nfit; /* Number of atoms in the reference/fit structure */
757 int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
759 real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
762 const char *TargetFile;
763 const char *OriginFile;
764 const char *EigvecFile;
768 /*to read topology file*/
774 gmx_bool bTop, bFit1;
777 { efTRN, "-f", "eigenvec", ffREAD },
778 { efXVG, "-eig", "eigenval", ffOPTRD },
779 { efTPS, NULL, NULL, ffREAD },
780 { efNDX, NULL, NULL, ffOPTRD },
781 { efSTX, "-tar", "target", ffOPTRD},
782 { efSTX, "-ori", "origin", ffOPTRD},
783 { efEDI, "-o", "sam", ffWRITE }
785 #define NFILE asize(fnm)
786 edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
787 if (!parse_common_args(&argc, argv, 0,
788 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
793 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
794 EdiFile = ftp2fn(efEDI, NFILE, fnm);
795 TargetFile = opt2fn_null("-tar", NFILE, fnm);
796 OriginFile = opt2fn_null("-ori", NFILE, fnm);
799 for (ev_class = 0; ev_class < evNr; ++ev_class)
801 if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
803 /*get list of eigenvectors*/
804 nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
805 if (ev_class < evStepNr-2)
807 /*if apropriate get list of stepsizes for these eigenvectors*/
808 if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
810 evStepList[ev_class] =
811 scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
813 else /*if list is not given fill with zeros */
815 snew(evStepList[ev_class], nvecs);
816 for (i = 0; i < nvecs; i++)
818 evStepList[ev_class][i] = 0.0;
822 else if (ev_class == evRADFIX)
824 snew(evStepList[ev_class], nvecs);
825 for (i = 0; i < nvecs; i++)
827 evStepList[ev_class][i] = radstep;
830 else if (ev_class == evFLOOD)
832 snew(evStepList[ev_class], nvecs);
834 /* Are we doing constant force flooding? In that case, we read in
835 * the fproj values from the command line */
836 if (opt2parg_bSet("-constF", NPA, pa))
838 evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
843 }; /*to avoid ambiguity */
845 else /* if there are no eigenvectors for this option set list to zero */
847 listen[ev_class] = NULL;
848 snew(listen[ev_class], 1);
849 listen[ev_class][0] = 0;
853 /* print the interpreted list of eigenvectors - to give some feedback*/
854 for (ev_class = 0; ev_class < evNr; ++ev_class)
856 printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
858 while (listen[ev_class][i])
860 printf("%d ", listen[ev_class][i++]);
866 EigvecFile = opt2fn("-f", NFILE, fnm);
868 /*read eigenvectors from eigvec.trr*/
869 read_eigenvectors(EigvecFile, &nav, &bFit1,
870 &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
872 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
873 title, &top, &ePBC, &xtop, NULL, topbox, 0);
877 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
878 get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
881 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
891 /* if g_covar used different coordinate groups to fit and to do the PCA */
892 printf("\nNote: the structure in %s should be the same\n"
893 " as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
894 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
898 printf("\nNote: Apparently no fitting was done in g_covar.\n"
899 " However, you need to select a reference group for fitting in mdrun\n");
901 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
903 for (i = 0; i < nfit; i++)
905 copy_rvec(xtop[ifit[i]], xref1[i]);
914 if (opt2parg_bSet("-constF", NPA, pa))
916 /* Constant force flooding is special: Most of the normal flooding
917 * options are not needed. */
918 edi_params.flood.bConstForce = TRUE;
922 /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
924 if (listen[evFLOOD][0] != 0)
926 read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T);
929 edi_params.flood.tau = tau;
930 edi_params.flood.deltaF0 = deltaF0;
931 edi_params.flood.deltaF = deltaF;
932 edi_params.presteps = eqSteps;
933 edi_params.flood.kT = kB*T;
934 edi_params.flood.bHarmonic = bHarmonic;
937 /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
938 edi_params.flood.constEfl = -constEfl;
939 edi_params.flood.alpha2 = -sqr(alpha);
943 edi_params.flood.constEfl = constEfl;
944 edi_params.flood.alpha2 = sqr(alpha);
948 edi_params.ned = nav;
950 /*number of system atoms */
951 edi_params.nini = atoms->nr;
954 /*store reference and average structure in edi_params*/
955 make_t_edx(&edi_params.sref, nfit, xref1, ifit );
956 make_t_edx(&edi_params.sav, nav, xav1, index);
959 /* Store target positions in edi_params */
960 if (opt2bSet("-tar", NFILE, fnm))
962 if (0 != listen[evFLOOD][0])
964 fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
965 " You may want to use -ori to define the flooding potential center.\n\n");
967 get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
971 make_t_edx(&edi_params.star, 0, NULL, index);
974 /* Store origin positions */
975 if (opt2bSet("-ori", NFILE, fnm))
977 get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
981 make_t_edx(&edi_params.sori, 0, NULL, index);
985 write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);