Remove gmx custom fixed int (e.g. gmx_int64_t) types

[gromacs.git] / src / gromacs / gmxana / gmx_make_edi.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
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 */
/* The make_edi program was generously contributed by Oliver Lange, based
 * on the code from g_anaeig. You can reach him as olange@gwdg.de. He
 * probably also holds copyright to the following code.
 */
#include "gmxpre.h"

#include <cctype>
#include <cmath>
#include <cstdlib>
#include <cstring>

#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/eigio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"

typedef struct
{
    real        deltaF0;
    gmx_bool    bHarmonic;
    gmx_bool    bConstForce;   /* Do constant force flooding instead of
                                  evaluating a flooding potential             */
    real        tau;
    real        deltaF;
    real        kT;
    real        constEfl;
    real        alpha2;
} t_edflood;


/* This type is for the average, reference, target, and origin structure   */
typedef struct edix
{
    int          nr;            /* number of atoms this structure contains */
    int         *anrs;          /* atom index numbers                      */
    rvec        *x;             /* positions                               */
    real        *sqrtm;         /* sqrt of the masses used for mass-
                                 * weighting of analysis                   */
} t_edix;


typedef struct edipar
{
    int         nini;           /* total Nr of atoms                    */
    gmx_bool    fitmas;         /* true if trans fit with cm            */
    gmx_bool    pcamas;         /* true if mass-weighted PCA            */
    int         presteps;       /* number of steps to run without any
                                 *    perturbations ... just monitoring */
    int         outfrq;         /* freq (in steps) of writing to edo    */
    int         maxedsteps;     /* max nr of steps per cycle            */
    struct edix sref;           /* reference positions, to these fitting
                                 * will be done                         */
    struct edix sav;            /* average positions                    */
    struct edix star;           /* target positions                     */
    struct edix sori;           /* origin positions                     */
    real        slope;          /* minimal slope in acceptance radexp   */
    int         ned;            /* Nr of atoms in essdyn buffer         */
    t_edflood   flood;          /* parameters especially for flooding   */
} t_edipar;



static void make_t_edx(struct edix *edx, int natoms, rvec *pos, int index[])
{
    edx->nr   = natoms;
    edx->anrs = index;
    edx->x    = pos;
}

static void write_t_edx(FILE *fp, struct edix edx, const char *comment)
{
    /*here we copy only the pointers into the t_edx struct
       no data is copied and edx.box is ignored  */
    int i;
    fprintf(fp, "#%s \n %d \n", comment, edx.nr);
    for (i = 0; i < edx.nr; i++)
    {
        fprintf(fp, "%d  %f  %f  %f\n", (edx.anrs)[i]+1, (edx.x)[i][XX], (edx.x)[i][YY], (edx.x)[i][ZZ]);
    }
}

static int sscan_list(int *list[], const char *str, const char *listname)
{
    /*this routine scans a string of the form 1,3-6,9 and returns the
       selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
       memory for this list will be allocated  in this routine -- sscan_list expects *list to
       be a NULL-Pointer

       listname is a string used in the errormessage*/


    int   i, istep;
    char  c;
    char *pos, *startpos, *step;
    int   n = std::strlen(str);

    /*enums to define the different lexical stati */
    enum {
        sBefore, sNumber, sMinus, sRange, sZero, sSmaller, sError, sSteppedRange
    };

    int   status     = sBefore; /*status of the deterministic automat to scan str   */
    int   number     = 0;
    int   end_number = 0;

    char *start = nullptr; /*holds the string of the number behind a ','*/
    char *end   = nullptr; /*holds the string of the number behind a '-' */

    int   nvecs = 0;       /* counts the number of vectors in the list*/

    step = nullptr;
    snew(pos, n+4);
    startpos = pos;
    std::strcpy(pos, str);
    pos[n]   = ',';
    pos[n+1] = '1';
    pos[n+2] = '\0';

    *list = nullptr;

    while ((c = *pos) != 0)
    {
        switch (status)
        {
            /* expect a number */
            case sBefore:
                if (std::isdigit(c))
                {
                    start  = pos;
                    status = sNumber;
                    break;
                }
                else
                {
                    status = sError;
                }
                break;

            /* have read a number, expect ',' or '-' */
            case sNumber:
                if (c == ',')
                {
                    /*store number*/
                    srenew(*list, nvecs+1);
                    (*list)[nvecs++] = number = std::strtol(start, nullptr, 10);
                    status           = sBefore;
                    if (number == 0)
                    {
                        status = sZero;
                    }
                    break;
                }
                else if (c == '-')
                {
                    status = sMinus; break;
                }
                else if (std::isdigit(c))
                {
                    break;
                }
                else
                {
                    status = sError;
                }
                break;

            /* have read a '-' -> expect a number */
            case sMinus:
                if (std::isdigit(c))
                {
                    end    = pos;
                    status = sRange; break;
                }
                else
                {
                    status = sError;
                }
                break;

            case sSteppedRange:
                if (std::isdigit(c))
                {
                    if (step)
                    {
                        status = sError; break;
                    }
                    else
                    {
                        step = pos;
                    }
                    status = sRange;
                    break;
                }
                else
                {
                    status = sError;
                }
                break;

            /* have read the number after a minus, expect ',' or ':' */
            case sRange:
                if (c == ',')
                {
                    /*store numbers*/
                    end_number = std::strtol(end, nullptr, 10);
                    number     = std::strtol(start, nullptr, 10);
                    status     = sBefore;
                    if (number == 0)
                    {
                        status = sZero; break;
                    }
                    if (end_number <= number)
                    {
                        status = sSmaller; break;
                    }
                    srenew(*list, nvecs+end_number-number+1);
                    if (step)
                    {
                        istep = strtol(step, nullptr, 10);
                        step  = nullptr;
                    }
                    else
                    {
                        istep = 1;
                    }
                    for (i = number; i <= end_number; i += istep)
                    {
                        (*list)[nvecs++] = i;
                    }
                    break;
                }
                else if (c == ':')
                {
                    status = sSteppedRange;
                    break;
                }
                else if (std::isdigit(c))
                {
                    break;
                }
                else
                {
                    status = sError;
                }
                break;

            /* format error occured */
            case sError:
                gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %ld with char %c", listname, pos-startpos, *(pos-1));
            /* logical error occured */
            case sZero:
                gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %ld: eigenvector 0 is not valid", listname, pos-startpos);
            case sSmaller:
                gmx_fatal(FARGS, "Error in the list of eigenvectors for %s at pos %ld: second index %d is not bigger than %d", listname, pos-startpos, end_number, number);
        }
        ++pos; /* read next character */
    }          /*scanner has finished */

    /* append zero to list of eigenvectors */
    srenew(*list, nvecs+1);
    (*list)[nvecs] = 0;
    sfree(startpos);
    return nvecs;
} /*sscan_list*/

static void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
{
/* eig_list is a zero-terminated list of indices into the eigvecs array.
   eigvecs are coordinates of eigenvectors
   grouptitle to write in the comment line
   steps  -- array with stepsizes for evLINFIX, evLINACC and evRADACC
 */

    int  n = 0, i; rvec x;
    while (eig_list[n++])
    {
        ;                 /*count selected eigenvecs*/

    }
    fprintf(fp, "# NUMBER OF EIGENVECTORS + %s\n %d\n", grouptitle, n-1);

    /* write list of eigenvector indicess */
    for (n = 0; eig_list[n]; n++)
    {
        if (steps)
        {
            fprintf(fp, "%8d   %g\n", eig_list[n], steps[n]);
        }
        else
        {
            fprintf(fp, "%8d   %g\n", eig_list[n], 1.0);
        }
    }
    n = 0;

    /* dump coordinates of the selected eigenvectors */
    while (eig_list[n])
    {
        for (i = 0; i < natoms; i++)
        {
            if (eig_list[n] > nvec)
            {
                gmx_fatal(FARGS, "Selected eigenvector %d is higher than maximum number %d of available eigenvectors", eig_list[n], nvec);
            }
            copy_rvec(eigvecs[eig_list[n]-1][i], x);
            fprintf(fp, "%8.5f %8.5f %8.5f\n", x[XX], x[YY], x[ZZ]);
        }
        n++;
    }
}


/*enum referring to the different lists of eigenvectors*/
enum {
    evLINFIX, evLINACC, evFLOOD, evRADFIX, evRADACC, evRADCON, evMON,  evNr
};
#define oldMAGIC 666
#define MAGIC 670


static void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
                                  int nvec, int *eig_listen[], real* evStepList[])
{
/* write edi-file */

    /*Header*/
    fprintf(fp, "#MAGIC\n %d \n#NINI\n %d\n#FITMAS\n %d\n#ANALYSIS_MAS\n %d\n",
            MAGIC, edpars->nini, int(edpars->fitmas), int(edpars->pcamas));
    fprintf(fp, "#OUTFRQ\n %d\n#MAXLEN\n %d\n#SLOPECRIT\n %f\n",
            edpars->outfrq, edpars->maxedsteps, edpars->slope);
    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",
            edpars->presteps, edpars->flood.deltaF0, edpars->flood.deltaF, edpars->flood.tau, edpars->flood.constEfl,
            edpars->flood.alpha2, edpars->flood.kT, int(edpars->flood.bHarmonic), int(edpars->flood.bConstForce));

    /* Average and reference positions */
    write_t_edx(fp, edpars->sref, "NREF, XREF");
    write_t_edx(fp, edpars->sav, "NAV, XAV");

    /*Eigenvectors */

    write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", nullptr);
    write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
    write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
    write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
    write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", nullptr);
    write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", nullptr);
    write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);


    /*Target and Origin positions */
    write_t_edx(fp, edpars->star, "NTARGET, XTARGET");
    write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
}

static int read_conffile(const char *confin, rvec **x)
{
    t_topology  top;
    matrix      box;
    printf("read coordnumber from file %s\n", confin);
    read_tps_conf(confin, &top, nullptr, x, nullptr, box, FALSE);
    printf("number of coordinates in file %d\n", top.atoms.nr);
    return top.atoms.nr;
}


static void read_eigenvalues(const int vecs[], const char *eigfile, real values[],
                             gmx_bool bHesse, real kT, int natoms_average_struct)
{
    int      neig, nrow, i;
    double **eigval;

    neig = read_xvg(eigfile, &eigval, &nrow);

    fprintf(stderr, "Read %d eigenvalues\n", neig);
    for (i = bHesse ? 6 : 0; i < neig; i++)
    {
        if (eigval[1][i] < -0.001 && bHesse)
        {
            fprintf(stderr,
                    "WARNING: The Hessian Matrix has negative eigenvalue %f, we set it to zero (no flooding in this direction)\n\n", eigval[1][i]);
        }

        if (eigval[1][i] < 0)
        {
            eigval[1][i] = 0;
        }
    }
    if (bHesse)
    {
        for (i = 0; vecs[i]; i++)
        {
            if (vecs[i] < 7)
            {
                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");
            }
            values[i] = eigval[1][vecs[i]-1]/kT;
        }
    }
    else
    {
        for (i = 0; vecs[i]; i++)
        {
            /* Make sure this eigenvalue does not correspond to one of the last 6 eigenvectors of the
             * covariance matrix. These correspond to the rotational and translational degrees of
             * freedom and will be zero within numerical accuracy.
             *
             * Note that the total number of eigenvectors produced by gmx covar depends on:
             * 1) the total number of degrees of freedom of the system (3N, with N the number of atoms)
             * 2) the number S of independent configurations fed into gmx covar.
             * For long trajectories with lots of frames, usually S >= 3N + 1, so that one indeed gets
             * 3N eigenvalues (of which the last 6 will have zero eigenvalues).
             * For S < 3N + 1, however, the covariance matrix becomes rank deficient, and the number
             * of possible eigenvalues is just S - 1. Since in make_edi we only know N but not S, we can
             * only warn the user if he picked one of the last 6 of 3N.
             */
            if (vecs[i] > ( 3 * natoms_average_struct - 6 ))
            {
                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");
            }
            values[i] = 1/eigval[1][vecs[i]-1];
        }
    }
    /* free memory */
    for (i = 0; i < nrow; i++)
    {
        sfree(eigval[i]);
    }
    sfree(eigval);
}


static real *scan_vecparams(const char *str, const char * par, int nvecs)
{
    char    f0[256], f1[256];         /*format strings adapted every pass of the loop*/
    double  d;
    int     i;
    real   *vec_params;

    snew(vec_params, nvecs);
    if (str)
    {
        f0[0] = '\0';
        for (i = 0; (i < nvecs); i++)
        {
            std::strcpy(f1, f0);    /*f0 is the format string for the "to-be-ignored" numbers*/
            std::strcat(f1, "%lf"); /*and f1 to read the actual number in this pass of the loop*/
            if (sscanf(str, f1, &d) != 1)
            {
                gmx_fatal(FARGS, "Not enough elements for %s parameter (I need %d)", par, nvecs);
            }
            vec_params[i] = d;
            std::strcat(f0, "%*s");
        }
    }
    return vec_params;
}


static void init_edx(struct edix *edx)
{
    edx->nr = 0;
    snew(edx->x, 1);
    snew(edx->anrs, 1);
}

static void filter2edx(struct edix *edx, int nindex, int index[], int ngro,
                       const int igro[], const rvec *x, const char* structure)
{
/* filter2edx copies coordinates from x to edx which are given in index
 */

    int pos, i;
    int ix = edx->nr;
    edx->nr += nindex;
    srenew(edx->x, edx->nr);
    srenew(edx->anrs, edx->nr);
    for (i = 0; i < nindex; i++, ix++)
    {
        for (pos = 0; pos < ngro-1 && igro[pos] != index[i]; ++pos)
        {
        }
        ;                                                            /*search element in igro*/
        if (igro[pos] != index[i])
        {
            gmx_fatal(FARGS, "Couldn't find atom with index %d in structure %s", index[i], structure);
        }
        edx->anrs[ix] = index[i];
        copy_rvec(x[pos], edx->x[ix]);
    }
}

static void get_structure(const t_atoms *atoms, const char *IndexFile,
                          const char *StructureFile, struct edix *edx, int nfit,
                          int ifit[], int nav, int index[])
{
    int     *igro; /*index corresponding to target or origin structure*/
    int      ngro;
    int      ntar;
    rvec    *xtar;
    char   * grpname;


    ntar = read_conffile(StructureFile, &xtar);
    printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
           ntar, StructureFile);
    get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
    if (ngro != ntar)
    {
        gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
    }
    init_edx(edx);
    filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);

    /* If average and reference/fitting structure differ, append the average structure as well */
    if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
    {
        filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
    }
}

int gmx_make_edi(int argc, char *argv[])
{

    static const char *desc[] = {
        "[THISMODULE] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
        "based on eigenvectors of a covariance matrix ([gmx-covar]) or from a",
        "normal modes analysis ([gmx-nmeig]).",
        "ED sampling can be used to manipulate the position along collective coordinates",
        "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
        "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
        "the system to explore new regions along these collective coordinates. A number",
        "of different algorithms are implemented to drive the system along the eigenvectors",
        "([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
        "to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
        "or to only monitor the projections of the positions onto",
        "these coordinates ([TT]-mon[tt]).[PAR]",
        "References:[PAR]",
        "A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
        "H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
        "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[PAR]",
        "B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
        "Towards an exhaustive sampling of the configurational spaces of the ",
        "two forms of the peptide hormone guanylin,",
        "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[PAR]",
        "B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
        "An extended sampling of the configurational space of HPr from E. coli",
        "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
        "[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
        "reference structure, target positions, etc.[PAR]",

        "[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
        "[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
        "[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
        "(steps in the desired directions will be accepted, others will be rejected).[PAR]",
        "[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
        "[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
        "(steps in the desired direction will be accepted, others will be rejected).",
        "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
        "expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
        "to read in a structure file that defines an external origin.[PAR]",
        "[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
        "towards a target structure specified with [TT]-tar[tt].[PAR]",
        "NOTE: each eigenvector can be selected only once. [PAR]",
        "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [REF].xvg[ref] file[PAR]",
        "[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
        "cycle will be started if the spontaneous increase of the radius (in nm/step)",
        "is less than the value specified.[PAR]",
        "[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
        "before a new cycle is started.[PAR]",
        "Note on the parallel implementation: since ED sampling is a 'global' thing",
        "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
        "is not very parallel-friendly from an implementation point of view. Because",
        "parallel ED requires some extra communication, expect the performance to be",
        "lower as in a free MD simulation, especially on a large number of ranks and/or",
        "when the ED group contains a lot of atoms. [PAR]",
        "Please also note that if your ED group contains more than a single protein,",
        "then the [REF].tpr[ref] file must contain the correct PBC representation of the ED group.",
        "Take a look on the initial RMSD from the reference structure, which is printed",
        "out at the start of the simulation; if this is much higher than expected, one",
        "of the ED molecules might be shifted by a box vector. [PAR]",
        "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [REF].xvg[ref] file",
        "as a function of time in intervals of OUTFRQ steps.[PAR]",
        "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
        "a single simulation (on different molecules) if several [REF].edi[ref] files were concatenated",
        "first. The constraints are applied in the order they appear in the [REF].edi[ref] file. ",
        "Depending on what was specified in the [REF].edi[ref] input file, the output file contains for each ED dataset",
        "",
        " * the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)",
        " * projections of the positions onto selected eigenvectors",
        "",
        "FLOODING:[PAR]",
        "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
        "which will lead to extra forces expelling the structure out of the region described",
        "by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
        "is kept in that region.",
        "[PAR]",
        "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
        "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
        "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
        "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
        "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
        "DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
        "To use constant Efl set [TT]-tau[tt] to zero.",
        "[PAR]",
        "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
        "to give good results for most standard cases in flooding of proteins.",
        "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
        "increase, this is mimicked by [GRK]alpha[grk] > 1.",
        "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
        "[PAR]",
        "RESTART and FLOODING:",
        "If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
        "the output file and manually put them into the [REF].edi[ref] file under DELTA_F0 and EFL_NULL."
    };

    /* Save all the params in this struct and then save it in an edi file.
     * ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
     */
    static t_edipar edi_params;

    enum  {
        evStepNr = evRADFIX + 1
    };
    static const char* evSelections[evNr]      = {nullptr, nullptr, nullptr, nullptr, nullptr, nullptr};
    static const char* evOptions[evNr]         = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
    static const char* evParams[evStepNr]      = {nullptr, nullptr};
    static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
    static const char* ConstForceStr;
    static real      * evStepList[evStepNr];
    static real        radstep  = 0.0;
    static real        deltaF0  = 150;
    static real        deltaF   = 0;
    static real        tau      = .1;
    static real        constEfl = 0.0;
    static real        alpha    = 1;
    static int         eqSteps  = 0;
    static int       * listen[evNr];
    static real        T         = 300.0;
    const real         kB        = 2.5 / 300.0; /* k_boltzmann in MD units */
    static gmx_bool    bRestrain = FALSE;
    static gmx_bool    bHesse    = FALSE;
    static gmx_bool    bHarmonic = FALSE;
    t_pargs            pa[]      = {
        { "-mon", FALSE, etSTR, {&evSelections[evMON]},
          "Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
        { "-linfix", FALSE, etSTR, {&evSelections[0]},
          "Indices of eigenvectors for fixed increment linear sampling" },
        { "-linacc", FALSE, etSTR, {&evSelections[1]},
          "Indices of eigenvectors for acceptance linear sampling" },
        { "-radfix", FALSE, etSTR, {&evSelections[3]},
          "Indices of eigenvectors for fixed increment radius expansion" },
        { "-radacc", FALSE, etSTR, {&evSelections[4]},
          "Indices of eigenvectors for acceptance radius expansion" },
        { "-radcon", FALSE, etSTR, {&evSelections[5]},
          "Indices of eigenvectors for acceptance radius contraction" },
        { "-flood",  FALSE, etSTR, {&evSelections[2]},
          "Indices of eigenvectors for flooding"},
        { "-outfrq", FALSE, etINT, {&edi_params.outfrq},
          "Frequency (in steps) of writing output in [REF].xvg[ref] file" },
        { "-slope", FALSE, etREAL, { &edi_params.slope},
          "Minimal slope in acceptance radius expansion"},
        { "-linstep", FALSE, etSTR, {&evParams[0]},
          "Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
        { "-accdir", FALSE, etSTR, {&evParams[1]},
          "Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
        { "-radstep", FALSE, etREAL, {&radstep},
          "Stepsize (nm/step) for fixed increment radius expansion"},
        { "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
          "Maximum number of steps per cycle" },
        { "-eqsteps", FALSE, etINT, {&eqSteps},
          "Number of steps to run without any perturbations "},
        { "-deltaF0", FALSE, etREAL, {&deltaF0},
          "Target destabilization energy for flooding"},
        { "-deltaF", FALSE, etREAL, {&deltaF},
          "Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
        { "-tau", FALSE, etREAL, {&tau},
          "Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
        { "-Eflnull", FALSE, etREAL, {&constEfl},
          "The starting value of the flooding strength. The flooding strength is updated "
          "according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
        { "-T", FALSE, etREAL, {&T},
          "T is temperature, the value is needed if you want to do flooding "},
        { "-alpha", FALSE, etREAL, {&alpha},
          "Scale width of gaussian flooding potential with alpha^2 "},
        { "-restrain", FALSE, etBOOL, {&bRestrain},
          "Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
        { "-hessian", FALSE, etBOOL, {&bHesse},
          "The eigenvectors and eigenvalues are from a Hessian matrix"},
        { "-harmonic", FALSE, etBOOL, {&bHarmonic},
          "The eigenvalues are interpreted as spring constant"},
        { "-constF", FALSE, etSTR, {&ConstForceStr},
          "Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
          "(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
    };
#define NPA asize(pa)

    rvec             *xref1;
    int               nvec1, *eignr1 = nullptr;
    rvec             *xav1, **eigvec1 = nullptr;
    t_atoms          *atoms = nullptr;
    int               nav; /* Number of atoms in the average structure */
    char             *grpname;
    const char       *indexfile;
    int               i;
    int              *index, *ifit;
    int               nfit;              /* Number of atoms in the reference/fit structure */
    int               ev_class;          /* parameter _class i.e. evMON, evRADFIX etc. */
    int               nvecs;
    real             *eigval1 = nullptr; /* in V3.3 this is parameter of read_eigenvectors */

    const char       *EdiFile;
    const char       *TargetFile;
    const char       *OriginFile;
    const char       *EigvecFile;

    gmx_output_env_t *oenv;

    /*to read topology file*/
    t_topology  top;
    int         ePBC;
    matrix      topbox;
    rvec       *xtop;
    gmx_bool    bFit1;

    t_filenm    fnm[] = {
        { efTRN, "-f",    "eigenvec",    ffREAD  },
        { efXVG, "-eig",  "eigenval",    ffOPTRD },
        { efTPS, nullptr,    nullptr,          ffREAD },
        { efNDX, nullptr,    nullptr,  ffOPTRD },
        { efSTX, "-tar", "target", ffOPTRD},
        { efSTX, "-ori", "origin", ffOPTRD},
        { efEDI, "-o", "sam", ffWRITE }
    };
#define NFILE asize(fnm)
    edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
    if (!parse_common_args(&argc, argv, 0,
                           NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
    {
        return 0;
    }

    indexfile       = ftp2fn_null(efNDX, NFILE, fnm);
    EdiFile         = ftp2fn(efEDI, NFILE, fnm);
    TargetFile      = opt2fn_null("-tar", NFILE, fnm);
    OriginFile      = opt2fn_null("-ori", NFILE, fnm);


    for (ev_class = 0; ev_class < evNr; ++ev_class)
    {
        if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
        {
            /*get list of eigenvectors*/
            nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
            if (ev_class < evStepNr-2)
            {
                /*if apropriate get list of stepsizes for these eigenvectors*/
                if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
                {
                    evStepList[ev_class] =
                        scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
                }
                else   /*if list is not given fill with zeros */
                {
                    snew(evStepList[ev_class], nvecs);
                    for (i = 0; i < nvecs; i++)
                    {
                        evStepList[ev_class][i] = 0.0;
                    }
                }
            }
            else if (ev_class == evRADFIX)
            {
                snew(evStepList[ev_class], nvecs);
                for (i = 0; i < nvecs; i++)
                {
                    evStepList[ev_class][i] = radstep;
                }
            }
            else if (ev_class == evFLOOD)
            {
                snew(evStepList[ev_class], nvecs);

                /* Are we doing constant force flooding? In that case, we read in
                 * the fproj values from the command line */
                if (opt2parg_bSet("-constF", NPA, pa))
                {
                    evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
                }
            }
            else
            {
            };   /*to avoid ambiguity   */
        }
        else     /* if there are no eigenvectors for this option set list to zero */
        {
            listen[ev_class] = nullptr;
            snew(listen[ev_class], 1);
            listen[ev_class][0] = 0;
        }
    }

    /* print the interpreted list of eigenvectors - to give some feedback*/
    for (ev_class = 0; ev_class < evNr; ++ev_class)
    {
        printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
        i = 0;
        while (listen[ev_class][i])
        {
            printf("%d ", listen[ev_class][i++]);
        }
        printf("\n");
    }

    EigvecFile = opt2fn("-f", NFILE, fnm);

    /*read eigenvectors from eigvec.trr*/
    read_eigenvectors(EigvecFile, &nav, &bFit1,
                      &xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);

    read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
                  &top, &ePBC, &xtop, nullptr, topbox, 0);
    atoms = &top.atoms;


    printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
    get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
    if (i != nav)
    {
        gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
                  i, nav);
    }
    printf("\n");


    if (xref1 == nullptr)
    {
        if (bFit1)
        {
            /* if g_covar used different coordinate groups to fit and to do the PCA */
            printf("\nNote: the structure in %s should be the same\n"
                   "      as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
            printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
        }
        else
        {
            printf("\nNote: Apparently no fitting was done in g_covar.\n"
                   "      However, you need to select a reference group for fitting in mdrun\n");
        }
        get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
        snew(xref1, nfit);
        for (i = 0; i < nfit; i++)
        {
            copy_rvec(xtop[ifit[i]], xref1[i]);
        }
    }
    else
    {
        nfit = nav;
        ifit = index;
    }

    if (opt2parg_bSet("-constF", NPA, pa))
    {
        /* Constant force flooding is special: Most of the normal flooding
         * options are not needed. */
        edi_params.flood.bConstForce = TRUE;
    }
    else
    {
        /* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */

        if (listen[evFLOOD][0] != 0)
        {
            read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T, nav);
        }

        edi_params.flood.tau       = tau;
        edi_params.flood.deltaF0   = deltaF0;
        edi_params.flood.deltaF    = deltaF;
        edi_params.presteps        = eqSteps;
        edi_params.flood.kT        = kB*T;
        edi_params.flood.bHarmonic = bHarmonic;
        if (bRestrain)
        {
            /* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
            edi_params.flood.constEfl = -constEfl;
            edi_params.flood.alpha2   = -gmx::square(alpha);
        }
        else
        {
            edi_params.flood.constEfl = constEfl;
            edi_params.flood.alpha2   = gmx::square(alpha);
        }
    }

    edi_params.ned = nav;

    /*number of system atoms  */
    edi_params.nini = atoms->nr;


    /*store reference and average structure in edi_params*/
    make_t_edx(&edi_params.sref, nfit, xref1, ifit );
    make_t_edx(&edi_params.sav, nav, xav1, index);


    /* Store target positions in edi_params */
    if (opt2bSet("-tar", NFILE, fnm))
    {
        if (0 != listen[evFLOOD][0])
        {
            fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
                    "      You may want to use -ori to define the flooding potential center.\n\n");
        }
        get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
    }
    else
    {
        make_t_edx(&edi_params.star, 0, nullptr, index);
    }

    /* Store origin positions */
    if (opt2bSet("-ori", NFILE, fnm))
    {
        get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
    }
    else
    {
        make_t_edx(&edi_params.sori, 0, nullptr, index);
    }

    /* Write edi-file */
    write_the_whole_thing(gmx_ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);

    return 0;
}