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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"
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"
74 gmx_bool bConstForce; /* Do constant force flooding instead of
75 evaluating a flooding potential */
84 /* This type is for the average, reference, target, and origin structure */
87 int nr; /* number of atoms this structure contains */
88 int *anrs; /* atom index numbers */
89 rvec *x; /* positions */
90 real *sqrtm; /* sqrt of the masses used for mass-
91 * weighting of analysis */
97 int nini; /* total Nr of atoms */
98 gmx_bool fitmas; /* true if trans fit with cm */
99 gmx_bool pcamas; /* true if mass-weighted PCA */
100 int presteps; /* number of steps to run without any
101 * perturbations ... just monitoring */
102 int outfrq; /* freq (in steps) of writing to edo */
103 int maxedsteps; /* max nr of steps per cycle */
104 struct edix sref; /* reference positions, to these fitting
106 struct edix sav; /* average positions */
107 struct edix star; /* target positions */
108 struct edix sori; /* origin positions */
109 real slope; /* minimal slope in acceptance radexp */
110 int ned; /* Nr of atoms in essdyn buffer */
111 t_edflood flood; /* parameters especially for flooding */
116 void make_t_edx(struct edix *edx, int natoms, rvec *pos, atom_id index[])
123 void write_t_edx(FILE *fp, struct edix edx, const char *comment)
125 /*here we copy only the pointers into the t_edx struct
126 no data is copied and edx.box is ignored */
128 fprintf(fp, "#%s \n %d \n", comment, edx.nr);
129 for (i = 0; i < edx.nr; i++)
131 fprintf(fp, "%d %f %f %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
135 int sscan_list(int *list[], const char *str, const char *listname)
137 /*this routine scans a string of the form 1,3-6,9 and returns the
138 selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
139 memory for this list will be allocated in this routine -- sscan_list expects *list to
142 listname is a string used in the errormessage*/
147 char *pos, *startpos, *step;
150 /*enums to define the different lexical stati */
152 sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
155 int status = sBefore; /*status of the deterministic automat to scan str */
159 char *start = NULL; /*holds the string of the number behind a ','*/
160 char *end = NULL; /*holds the string of the number behind a '-' */
162 int nvecs = 0; /* counts the number of vectors in the list*/
174 while ((c = *pos) != 0)
178 /* expect a number */
179 case sBefore: if (isdigit(c))
190 /* have read a number, expect ',' or '-' */
191 case sNumber: if (c == ',')
194 srenew(*list, nvecs+1);
195 (*list)[nvecs++] = number = strtol(start, NULL, 10);
205 status = sMinus; break;
216 /* have read a '-' -> expect a number */
221 status = sRange; break;
233 status = sError; break;
247 /* have read the number after a minus, expect ',' or ':' */
252 end_number = strtol(end, NULL, 10);
253 number = strtol(start, NULL, 10);
257 status = sZero; break;
259 if (end_number <= number)
261 status = sSmaller; break;
263 srenew(*list, nvecs+end_number-number+1);
266 istep = strtol(step, NULL, 10);
273 for (i = number; i <= end_number; i += istep)
275 (*list)[nvecs++] = i;
281 status = sSteppedRange;
293 /* format error occured */
295 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d with char %c", listname, pos-startpos, *(pos-1));
297 /* logical error occured */
299 gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %d: eigenvector 0 is not valid", listname, pos-startpos);
302 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);
305 ++pos; /* read next character */
306 } /*scanner has finished */
308 /* append zero to list of eigenvectors */
309 srenew(*list, nvecs+1);
315 void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
317 /* eig_list is a zero-terminated list of indices into the eigvecs array.
318 eigvecs are coordinates of eigenvectors
319 grouptitle to write in the comment line
320 steps -- array with stepsizes for evLINFIX, evLINACC and evRADACC
323 int n = 0, i; rvec x;
325 while (eig_list[n++])
327 ; /*count selected eigenvecs*/
330 fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);
332 /* write list of eigenvector indicess */
333 for (n = 0; eig_list[n]; n++)
337 fprintf(fp, "%8d %g\n", eig_list[n], steps[n]);
341 fprintf(fp, "%8d %g\n", eig_list[n], 1.0);
346 /* dump coordinates of the selected eigenvectors */
350 for (i = 0; i < natoms; i++)
352 if (eig_list[n] > nvec)
354 gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
356 copy_rvec(eigvecs[eig_list[n]-1][i], x);
358 fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
365 /*enum referring to the different lists of eigenvectors*/
367 evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON, evNr
373 void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
374 int nvec, int *eig_listen[], real* evStepList[])
379 fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
380 MAGIC, edpars->nini, edpars->fitmas, edpars->pcamas);
381 fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
382 edpars->outfrq, edpars->maxedsteps, edpars->slope);
383 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",
384 edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
385 edpars->flood.alpha2, edpars->flood.kT, edpars->flood.bHarmonic, edpars->flood.bConstForce);
387 /* Average and reference positions */
388 write_t_edx(fp, edpars->sref, "NREF, XREF");
389 write_t_edx(fp, edpars->sav, "NAV, XAV");
393 write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", NULL);
394 write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
395 write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
396 write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
397 write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", NULL);
398 write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", NULL);
399 write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
402 /*Target and Origin positions */
403 write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
404 write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
407 int read_conffile(const char *confin, char *title, rvec *x[])
409 /* read coordinates out of STX file */
413 printf("read coordnumber from file %s\n", confin);
414 get_stx_coordnum(confin, &natoms);
415 printf("number of coordinates in file %d\n", natoms);
416 /* if (natoms != ncoords)
417 gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
418 " does not match topology (= %d)",
419 confin,natoms,ncoords);
421 /* make space for coordinates and velocities */
422 init_t_atoms(&confat, natoms, FALSE);
424 read_stx_conf(confin, title, &confat, *x, NULL, NULL, box);
429 void read_eigenvalues(int vecs[], const char *eigfile, real values[],
430 gmx_bool bHesse, real kT)
435 neig = read_xvg(eigfile, &eigval, &nrow);
437 fprintf(stderr, "Read %d eigenvalues\n", neig);
438 for (i = bHesse ? 6 : 0; i < neig; i++)
440 if (eigval[1][i] < -0.001 && bHesse)
443 "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
446 if (eigval[1][i] < 0)
453 for (i = 0; vecs[i]; i++)
457 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");
459 values[i] = eigval[1][vecs[i]-1]/kT;
464 for (i = 0; vecs[i]; i++)
466 if (vecs[i] > (neig-6))
468 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");
470 values[i] = 1/eigval[1][vecs[i]-1];
474 for (i = 0; i < nrow; i++)
482 static real *scan_vecparams(const char *str, const char * par, int nvecs)
484 char f0[256], f1[256]; /*format strings adapted every pass of the loop*/
489 snew(vec_params, nvecs);
493 for (i = 0; (i < nvecs); i++)
495 strcpy(f1, f0); /*f0 is the format string for the "to-be-ignored" numbers*/
496 strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
497 if (sscanf(str, f1, &d) != 1)
499 gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
510 void init_edx(struct edix *edx)
517 void filter2edx(struct edix *edx, int nindex, atom_id index[], int ngro,
518 atom_id igro[], rvec *x, const char* structure)
520 /* filter2edx copies coordinates from x to edx which are given in index
526 srenew(edx->x, edx->nr);
527 srenew(edx->anrs, edx->nr);
528 for (i = 0; i < nindex; i++, ix++)
530 for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
533 ; /*search element in igro*/
534 if (igro[pos] != index[i])
536 gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
538 edx->anrs[ix] = index[i];
539 copy_rvec(x[pos], edx->x[ix]);
543 void get_structure(t_atoms *atoms, const char *IndexFile,
544 const char *StructureFile, struct edix *edx, int nfit,
545 atom_id ifit[], int nav, atom_id index[])
547 atom_id *igro; /*index corresponding to target or origin structure*/
555 ntar = read_conffile(StructureFile, title, &xtar);
556 printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
557 ntar, StructureFile);
558 get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
561 gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
564 filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
566 /* If average and reference/fitting structure differ, append the average structure as well */
567 if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
569 filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
573 int gmx_make_edi(int argc, char *argv[])
576 static const char *desc[] = {
577 "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
578 "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
579 "normal modes analysis ([gmx-nmeig]).",
580 "ED sampling can be used to manipulate the position along collective coordinates",
581 "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
582 "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
583 "the system to explore new regions along these collective coordinates. A number",
584 "of different algorithms are implemented to drive the system along the eigenvectors",
585 "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
586 "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
587 "or to only monitor the projections of the positions onto",
588 "these coordinates ([TT]-mon[tt]).[PAR]",
590 "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
591 "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
592 "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
593 "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
594 "Towards an exhaustive sampling of the configurational spaces of the ",
595 "two forms of the peptide hormone guanylin,",
596 "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
597 "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
598 "An extended sampling of the configurational space of HPr from E. coli",
599 "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
600 "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
601 "reference structure, target positions, etc.[PAR]",
603 "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
604 "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
605 "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
606 "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
607 "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
608 "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
609 "(steps in the desired direction will be accepted, others will be rejected).",
610 "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
611 "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
612 "to read in a structure file that defines an external origin.[PAR]",
613 "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
614 "towards a target structure specified with [TT]-tar[tt].[PAR]",
615 "NOTE: each eigenvector can be selected only once. [PAR]",
616 "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
617 "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
618 "cycle will be started if the spontaneous increase of the radius (in nm/step)",
619 "is less than the value specified.[PAR]",
620 "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
621 "before a new cycle is started.[PAR]",
622 "Note on the parallel implementation: since ED sampling is a 'global' thing",
623 "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
624 "is not very parallel-friendly from an implementation point of view. Because",
625 "parallel ED requires some extra communication, expect the performance to be",
626 "lower as in a free MD simulation, especially on a large number of nodes and/or",
627 "when the ED group contains a lot of atoms. [PAR]",
628 "Please also note that if your ED group contains more than a single protein,",
629 "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
630 "Take a look on the initial RMSD from the reference structure, which is printed",
631 "out at the start of the simulation; if this is much higher than expected, one",
632 "of the ED molecules might be shifted by a box vector. [PAR]",
633 "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
634 "as a function of time in intervals of OUTFRQ steps.[PAR]",
635 "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
636 "a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
637 "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
638 "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
639 "[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
640 "[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
643 "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
644 "which will lead to extra forces expelling the structure out of the region described",
645 "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
646 "is kept in that region.",
648 "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
649 "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
650 "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
651 "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
652 "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
653 "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
654 "To use constant Efl set [TT]-tau[tt] to zero.",
656 "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
657 "to give good results for most standard cases in flooding of proteins.",
658 "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
659 "increase, this is mimicked by [GRK]alpha[grk] > 1.",
660 "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
662 "RESTART and FLOODING:",
663 "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
664 "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
667 /* Save all the params in this struct and then save it in an edi file.
668 * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
670 static t_edipar edi_params;
673 evStepNr = evRADFIX + 1
675 static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
676 static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
677 static const char* evParams[evStepNr] = {NULL, NULL};
678 static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
679 static const char* ConstForceStr;
680 static real * evStepList[evStepNr];
681 static real radfix = 0.0;
682 static real deltaF0 = 150;
683 static real deltaF = 0;
684 static real tau = .1;
685 static real constEfl = 0.0;
686 static real alpha = 1;
687 static int eqSteps = 0;
688 static int * listen[evNr];
689 static real T = 300.0;
690 const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
691 static gmx_bool bRestrain = FALSE;
692 static gmx_bool bHesse = FALSE;
693 static gmx_bool bHarmonic = FALSE;
695 { "-mon", FALSE, etSTR, {&evSelections[evMON]},
696 "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
697 { "-linfix", FALSE, etSTR, {&evSelections[0]},
698 "Indices of eigenvectors for fixed increment linear sampling" },
699 { "-linacc", FALSE, etSTR, {&evSelections[1]},
700 "Indices of eigenvectors for acceptance linear sampling" },
701 { "-radfix", FALSE, etSTR, {&evSelections[3]},
702 "Indices of eigenvectors for fixed increment radius expansion" },
703 { "-radacc", FALSE, etSTR, {&evSelections[4]},
704 "Indices of eigenvectors for acceptance radius expansion" },
705 { "-radcon", FALSE, etSTR, {&evSelections[5]},
706 "Indices of eigenvectors for acceptance radius contraction" },
707 { "-flood", FALSE, etSTR, {&evSelections[2]},
708 "Indices of eigenvectors for flooding"},
709 { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
710 "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
711 { "-slope", FALSE, etREAL, { &edi_params.slope},
712 "Minimal slope in acceptance radius expansion"},
713 { "-linstep", FALSE, etSTR, {&evParams[0]},
714 "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
715 { "-accdir", FALSE, etSTR, {&evParams[1]},
716 "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
717 { "-radstep", FALSE, etREAL, {&radfix},
718 "Stepsize (nm/step) for fixed increment radius expansion"},
719 { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
720 "Maximum number of steps per cycle" },
721 { "-eqsteps", FALSE, etINT, {&eqSteps},
722 "Number of steps to run without any perturbations "},
723 { "-deltaF0", FALSE, etREAL, {&deltaF0},
724 "Target destabilization energy for flooding"},
725 { "-deltaF", FALSE, etREAL, {&deltaF},
726 "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
727 { "-tau", FALSE, etREAL, {&tau},
728 "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
729 { "-Eflnull", FALSE, etREAL, {&constEfl},
730 "The starting value of the flooding strength. The flooding strength is updated "
731 "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
732 { "-T", FALSE, etREAL, {&T},
733 "T is temperature, the value is needed if you want to do flooding "},
734 { "-alpha", FALSE, etREAL, {&alpha},
735 "Scale width of gaussian flooding potential with alpha^2 "},
736 { "-restrain", FALSE, etBOOL, {&bRestrain},
737 "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
738 { "-hessian", FALSE, etBOOL, {&bHesse},
739 "The eigenvectors and eigenvalues are from a Hessian matrix"},
740 { "-harmonic", FALSE, etBOOL, {&bHarmonic},
741 "The eigenvalues are interpreted as spring constant"},
742 { "-constF", FALSE, etSTR, {&ConstForceStr},
743 "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
744 "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
746 #define NPA asize(pa)
749 int nvec1, *eignr1 = NULL;
750 rvec *xav1, **eigvec1 = NULL;
751 t_atoms *atoms = NULL;
752 int nav; /* Number of atoms in the average structure */
754 const char *indexfile;
756 atom_id *index, *ifit;
757 int nfit; /* Number of atoms in the reference/fit structure */
758 int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
760 real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
763 const char *TargetFile;
764 const char *OriginFile;
765 const char *EigvecFile;
769 /*to read topology file*/
775 gmx_bool bTop, bFit1;
778 { efTRN, "-f", "eigenvec", ffREAD },
779 { efXVG, "-eig", "eigenval", ffOPTRD },
780 { efTPS, NULL, NULL, ffREAD },
781 { efNDX, NULL, NULL, ffOPTRD },
782 { efSTX, "-tar", "target", ffOPTRD},
783 { efSTX, "-ori", "origin", ffOPTRD},
784 { efEDI, "-o", "sam", ffWRITE }
786 #define NFILE asize(fnm)
787 edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
788 if (!parse_common_args(&argc, argv, 0,
789 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
794 indexfile = ftp2fn_null(efNDX, NFILE, fnm);
795 EdiFile = ftp2fn(efEDI, NFILE, fnm);
796 TargetFile = opt2fn_null("-tar", NFILE, fnm);
797 OriginFile = opt2fn_null("-ori", NFILE, fnm);
800 for (ev_class = 0; ev_class < evNr; ++ev_class)
802 if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
804 /*get list of eigenvectors*/
805 nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
806 if (ev_class < evStepNr-2)
808 /*if apropriate get list of stepsizes for these eigenvectors*/
809 if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
811 evStepList[ev_class] =
812 scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
814 else /*if list is not given fill with zeros */
816 snew(evStepList[ev_class], nvecs);
817 for (i = 0; i < nvecs; i++)
819 evStepList[ev_class][i] = 0.0;
823 else if (ev_class == evRADFIX && opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
825 snew(evStepList[ev_class], nvecs);
826 for (i = 0; i < nvecs; i++)
828 evStepList[ev_class][i] = radfix;
831 else if (ev_class == evFLOOD)
833 snew(evStepList[ev_class], nvecs);
835 /* Are we doing constant force flooding? In that case, we read in
836 * the fproj values from the command line */
837 if (opt2parg_bSet("-constF", NPA, pa))
839 evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
844 }; /*to avoid ambiguity */
846 else /* if there are no eigenvectors for this option set list to zero */
848 listen[ev_class] = NULL;
849 snew(listen[ev_class], 1);
850 listen[ev_class][0] = 0;
854 /* print the interpreted list of eigenvectors - to give some feedback*/
855 for (ev_class = 0; ev_class < evNr; ++ev_class)
857 printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
859 while (listen[ev_class][i])
861 printf("%d ", listen[ev_class][i++]);
867 EigvecFile = opt2fn("-f", NFILE, fnm);
869 /*read eigenvectors from eigvec.trr*/
870 read_eigenvectors(EigvecFile, &nav, &bFit1,
871 &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
873 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
874 title, &top, &ePBC, &xtop, NULL, topbox, 0);
878 printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
879 get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
882 gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
892 /* if g_covar used different coordinate groups to fit and to do the PCA */
893 printf("\nNote: the structure in %s should be the same\n"
894 " as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
895 printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
899 printf("\nNote: Apparently no fitting was done in g_covar.\n"
900 " However, you need to select a reference group for fitting in mdrun\n");
902 get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
904 for (i = 0; i < nfit; i++)
906 copy_rvec(xtop[ifit[i]], xref1[i]);
915 if (opt2parg_bSet("-constF", NPA, pa))
917 /* Constant force flooding is special: Most of the normal flooding
918 * options are not needed. */
919 edi_params.flood.bConstForce = TRUE;
923 /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
925 if (listen[evFLOOD][0] != 0)
927 read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T);
930 edi_params.flood.tau = tau;
931 edi_params.flood.deltaF0 = deltaF0;
932 edi_params.flood.deltaF = deltaF;
933 edi_params.presteps = eqSteps;
934 edi_params.flood.kT = kB*T;
935 edi_params.flood.bHarmonic = bHarmonic;
938 /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
939 edi_params.flood.constEfl = -constEfl;
940 edi_params.flood.alpha2 = -sqr(alpha);
944 edi_params.flood.constEfl = constEfl;
945 edi_params.flood.alpha2 = sqr(alpha);
949 edi_params.ned = nav;
951 /*number of system atoms */
952 edi_params.nini = atoms->nr;
955 /*store reference and average structure in edi_params*/
956 make_t_edx(&edi_params.sref, nfit, xref1, ifit );
957 make_t_edx(&edi_params.sav, nav, xav1, index);
960 /* Store target positions in edi_params */
961 if (opt2bSet("-tar", NFILE, fnm))
963 if (0 != listen[evFLOOD][0])
965 fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
966 " You may want to use -ori to define the flooding potential center.\n\n");
968 get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
972 make_t_edx(&edi_params.star, 0, NULL, index);
975 /* Store origin positions */
976 if (opt2bSet("-ori", NFILE, fnm))
978 get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
982 make_t_edx(&edi_params.sori, 0, NULL, index);
986 write_the_whole_thing(ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);