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

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
 * Copyright (c) 2018,2019,2020, 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
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
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 * To help us fund GROMACS development, we humbly ask that you cite
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 */
#include "gmxpre.h"

#include "sfactor.h"

#include <cmath>
#include <cstring>

#include <algorithm>

#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.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"
#include "gromacs/utility/strdb.h"


typedef struct gmx_structurefactors
{
    int  nratoms;
    int* p; /* proton number */
    int* n; /* neutron number */
    /* Parameters for the Cromer Mann fit */
    real** a;      /* parameter a */
    real** b;      /* parameter b */
    real*  c;      /* parameter c */
    char** atomnm; /* atomname */

} gmx_structurefactors;

typedef struct reduced_atom
{
    rvec x;
    int  t;
} reduced_atom;


typedef struct structure_factor
{
    int      n_angles;
    int      n_groups;
    double   lambda;
    double   energy;
    double   momentum;
    double   ref_k;
    double** F;
    int      nSteps;
    int      total_n_atoms;
} structure_factor;


extern int* create_indexed_atom_type(reduced_atom_t* atm, int size)
{
    /*
     * create an index of the atom types found in a  group
     * i.e.: for water index_atp[0]=type_number_of_O and
     *                 index_atp[1]=type_number_of_H
     *
     * the last element is set to 0
     */
    int *index_atp, i, i_tmp, j;

    reduced_atom* att = static_cast<reduced_atom*>(atm);

    snew(index_atp, 1);
    i_tmp        = 1;
    index_atp[0] = att[0].t;
    for (i = 1; i < size; i++)
    {
        for (j = 0; j < i_tmp; j++)
        {
            if (att[i].t == index_atp[j])
            {
                break;
            }
        }
        if (j == i_tmp) /* i.e. no indexed atom type is  == to atm[i].t */
        {
            i_tmp++;
            srenew(index_atp, i_tmp * sizeof(int));
            index_atp[i_tmp - 1] = att[i].t;
        }
    }
    i_tmp++;
    srenew(index_atp, i_tmp * sizeof(int));
    index_atp[i_tmp - 1] = 0;
    return index_atp;
}


extern t_complex*** rc_tensor_allocation(int x, int y, int z)
{
    t_complex*** t;
    int          i, j;

    snew(t, x);
    snew(t[0], x * y);
    snew(t[0][0], x * y * z);

    for (j = 1; j < y; j++)
    {
        t[0][j] = t[0][j - 1] + z;
    }
    for (i = 1; i < x; i++)
    {
        t[i]    = t[i - 1] + y;
        t[i][0] = t[i - 1][0] + y * z;
        for (j = 1; j < y; j++)
        {
            t[i][j] = t[i][j - 1] + z;
        }
    }
    return t;
}


extern void compute_structure_factor(structure_factor_t* sft,
                                     matrix              box,
                                     reduced_atom_t*     red,
                                     int                 isize,
                                     real                start_q,
                                     real                end_q,
                                     int                 group,
                                     real**              sf_table)
{
    structure_factor* sf   = static_cast<structure_factor*>(sft);
    reduced_atom*     redt = static_cast<reduced_atom*>(red);

    t_complex*** tmpSF;
    rvec         k_factor;
    real         kdotx, asf, kx, ky, kz, krr;
    int          kr, maxkx, maxky, maxkz, i, j, k, p, *counter;


    k_factor[XX] = 2 * M_PI / box[XX][XX];
    k_factor[YY] = 2 * M_PI / box[YY][YY];
    k_factor[ZZ] = 2 * M_PI / box[ZZ][ZZ];

    maxkx = gmx::roundToInt(end_q / k_factor[XX]);
    maxky = gmx::roundToInt(end_q / k_factor[YY]);
    maxkz = gmx::roundToInt(end_q / k_factor[ZZ]);

    snew(counter, sf->n_angles);

    tmpSF = rc_tensor_allocation(maxkx, maxky, maxkz);
    /*
     * The big loop...
     * compute real and imaginary part of the structure factor for every
     * (kx,ky,kz))
     */
    fprintf(stderr, "\n");
    for (i = 0; i < maxkx; i++)
    {
        fprintf(stderr, "\rdone %3.1f%%     ", (100.0 * (i + 1)) / maxkx);
        fflush(stderr);
        kx = i * k_factor[XX];
        for (j = 0; j < maxky; j++)
        {
            ky = j * k_factor[YY];
            for (k = 0; k < maxkz; k++)
            {
                if (i != 0 || j != 0 || k != 0)
                {
                    kz  = k * k_factor[ZZ];
                    krr = std::sqrt(gmx::square(kx) + gmx::square(ky) + gmx::square(kz));
                    if (krr >= start_q && krr <= end_q)
                    {
                        kr = gmx::roundToInt(krr / sf->ref_k);
                        if (kr < sf->n_angles)
                        {
                            counter[kr]++; /* will be used for the copmutation
                                              of the average*/
                            for (p = 0; p < isize; p++)
                            {
                                asf = sf_table[redt[p].t][kr];

                                kdotx = kx * redt[p].x[XX] + ky * redt[p].x[YY] + kz * redt[p].x[ZZ];

                                tmpSF[i][j][k].re += std::cos(kdotx) * asf;
                                tmpSF[i][j][k].im += std::sin(kdotx) * asf;
                            }
                        }
                    }
                }
            }
        }
    } /* end loop on i */
      /*
       *  compute the square modulus of the structure factor, averaging on the surface
       *  kx*kx + ky*ky + kz*kz = krr*krr
       *  note that this is correct only for a (on the macroscopic scale)
       *  isotropic system.
       */
    for (i = 0; i < maxkx; i++)
    {
        kx = i * k_factor[XX];
        for (j = 0; j < maxky; j++)
        {
            ky = j * k_factor[YY];
            for (k = 0; k < maxkz; k++)
            {
                kz  = k * k_factor[ZZ];
                krr = std::sqrt(gmx::square(kx) + gmx::square(ky) + gmx::square(kz));
                if (krr >= start_q && krr <= end_q)
                {
                    kr = gmx::roundToInt(krr / sf->ref_k);
                    if (kr < sf->n_angles && counter[kr] != 0)
                    {
                        sf->F[group][kr] +=
                                (gmx::square(tmpSF[i][j][k].re) + gmx::square(tmpSF[i][j][k].im))
                                / counter[kr];
                    }
                }
            }
        }
    }
    sfree(counter);
    sfree(tmpSF[0][0]);
    sfree(tmpSF[0]);
    sfree(tmpSF);
}


extern gmx_structurefactors_t* gmx_structurefactors_init(const char* datfn)
{

    /* Read the database for the structure factor of the different atoms */

    char                  line[STRLEN];
    gmx_structurefactors* gsf;
    double                a1, a2, a3, a4, b1, b2, b3, b4, c;
    int                   p;
    int                   i;
    int                   nralloc = 10;
    int                   line_no;
    char                  atomn[32];
    gmx::FilePtr          fp = gmx::openLibraryFile(datfn);
    line_no                  = 0;
    snew(gsf, 1);

    snew(gsf->atomnm, nralloc);
    snew(gsf->a, nralloc);
    snew(gsf->b, nralloc);
    snew(gsf->c, nralloc);
    snew(gsf->p, nralloc);
    gsf->n       = nullptr;
    gsf->nratoms = line_no;
    while (get_a_line(fp.get(), line, STRLEN))
    {
        i = line_no;
        if (sscanf(line, "%s %d %lf %lf %lf %lf %lf %lf %lf %lf %lf", atomn, &p, &a1, &a2, &a3, &a4,
                   &b1, &b2, &b3, &b4, &c)
            == 11)
        {
            gsf->atomnm[i] = gmx_strdup(atomn);
            gsf->p[i]      = p;
            snew(gsf->a[i], 4);
            snew(gsf->b[i], 4);
            gsf->a[i][0] = a1;
            gsf->a[i][1] = a2;
            gsf->a[i][2] = a3;
            gsf->a[i][3] = a4;
            gsf->b[i][0] = b1;
            gsf->b[i][1] = b2;
            gsf->b[i][2] = b3;
            gsf->b[i][3] = b4;
            gsf->c[i]    = c;
            line_no++;
            gsf->nratoms = line_no;
            if (line_no == nralloc)
            {
                nralloc += 10;
                srenew(gsf->atomnm, nralloc);
                srenew(gsf->a, nralloc);
                srenew(gsf->b, nralloc);
                srenew(gsf->c, nralloc);
                srenew(gsf->p, nralloc);
            }
        }
        else
        {
            fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n", datfn, line_no);
        }
    }

    srenew(gsf->atomnm, gsf->nratoms);
    srenew(gsf->a, gsf->nratoms);
    srenew(gsf->b, gsf->nratoms);
    srenew(gsf->c, gsf->nratoms);
    srenew(gsf->p, gsf->nratoms);

    return static_cast<gmx_structurefactors_t*>(gsf);
}


extern void rearrange_atoms(reduced_atom_t*         positions,
                            t_trxframe*             fr,
                            const int*              index,
                            int                     isize,
                            const t_topology*       top,
                            gmx_bool                flag,
                            gmx_structurefactors_t* gsf)
/* given the group's index, return the (continuous) array of atoms */
{
    int i;

    reduced_atom* pos = static_cast<reduced_atom*>(positions);

    if (flag)
    {
        for (i = 0; i < isize; i++)
        {
            pos[i].t = return_atom_type(*(top->atoms.atomname[index[i]]), gsf);
        }
    }
    for (i = 0; i < isize; i++)
    {
        copy_rvec(fr->x[index[i]], pos[i].x);
    }
}


extern int return_atom_type(const char* name, gmx_structurefactors_t* gsf)
{
    typedef struct
    {
        const char* name;
        int         nh;
    } t_united_h;
    t_united_h uh[] = { { "CH1", 1 }, { "CH2", 2 }, { "CH3", 3 }, { "CS1", 1 }, { "CS2", 2 },
                        { "CS3", 3 }, { "CP1", 1 }, { "CP2", 2 }, { "CP3", 3 } };
    int        i, cnt = 0;
    int*       tndx;
    int        nrc;
    int        fndx = 0;
    int        NCMT;

    gmx_structurefactors* gsft = static_cast<gmx_structurefactors*>(gsf);

    NCMT = gsft->nratoms;

    snew(tndx, NCMT);

    for (i = 0; (i < asize(uh)); i++)
    {
        if (std::strcmp(name, uh[i].name) == 0)
        {
            return NCMT - 1 + uh[i].nh;
        }
    }

    for (i = 0; (i < NCMT); i++)
    {
        if (std::strncmp(name, gsft->atomnm[i], std::strlen(gsft->atomnm[i])) == 0)
        {
            tndx[cnt] = i;
            cnt++;
        }
    }

    if (cnt == 0)
    {
        gmx_fatal(FARGS, "\nError: atom (%s) not in list (%d types checked)!\n", name, i);
    }
    else
    {
        nrc = 0;
        for (i = 0; i < cnt; i++)
        {
            if (std::strlen(gsft->atomnm[tndx[i]]) > static_cast<size_t>(nrc))
            {
                nrc  = std::strlen(gsft->atomnm[tndx[i]]);
                fndx = tndx[i];
            }
        }

        return fndx;
    }
}

extern int gmx_structurefactors_get_sf(gmx_structurefactors_t* gsf, int elem, real a[4], real b[4], real* c)
{

    int                   success;
    int                   i;
    gmx_structurefactors* gsft = static_cast<gmx_structurefactors*>(gsf);
    success                    = 0;

    for (i = 0; i < 4; i++)
    {
        a[i] = gsft->a[elem][i];
        b[i] = gsft->b[elem][i];
        *c   = gsft->c[elem];
    }

    success += 1;
    return success;
}

extern int do_scattering_intensity(const char*             fnTPS,
                                   const char*             fnNDX,
                                   const char*             fnXVG,
                                   const char*             fnTRX,
                                   const char*             fnDAT,
                                   real                    start_q,
                                   real                    end_q,
                                   real                    energy,
                                   int                     ng,
                                   const gmx_output_env_t* oenv)
{
    int               i, *isize, flags = TRX_READ_X, **index_atp;
    t_trxstatus*      status;
    char**            grpname;
    int**             index;
    t_topology        top;
    PbcType           pbcType;
    t_trxframe        fr;
    reduced_atom_t**  red;
    structure_factor* sf;
    rvec*             xtop;
    real**            sf_table;
    matrix            box;
    real              r_tmp;

    gmx_structurefactors_t* gmx_sf;
    real *                  a, *b, c;

    snew(a, 4);
    snew(b, 4);


    gmx_sf = gmx_structurefactors_init(fnDAT);

    gmx_structurefactors_get_sf(gmx_sf, 0, a, b, &c);

    snew(sf, 1);
    sf->energy = energy;

    /* Read the topology informations */
    read_tps_conf(fnTPS, &top, &pbcType, &xtop, nullptr, box, TRUE);
    sfree(xtop);

    /* groups stuff... */
    snew(isize, ng);
    snew(index, ng);
    snew(grpname, ng);

    fprintf(stderr, "\nSelect %d group%s\n", ng, ng == 1 ? "" : "s");
    if (fnTPS)
    {
        get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
    }
    else
    {
        rd_index(fnNDX, ng, isize, index, grpname);
    }

    /* The first time we read data is a little special */
    read_first_frame(oenv, &status, fnTRX, &fr, flags);

    sf->total_n_atoms = fr.natoms;

    snew(red, ng);
    snew(index_atp, ng);

    r_tmp = std::max(box[XX][XX], box[YY][YY]);
    r_tmp = std::max(box[ZZ][ZZ], r_tmp);

    sf->ref_k = (2.0 * M_PI) / (r_tmp);
    /* ref_k will be the reference momentum unit */
    sf->n_angles = gmx::roundToInt(end_q / sf->ref_k);

    snew(sf->F, ng);
    for (i = 0; i < ng; i++)
    {
        snew(sf->F[i], sf->n_angles);
    }
    for (i = 0; i < ng; i++)
    {
        snew(red[i], isize[i]);
        rearrange_atoms(red[i], &fr, index[i], isize[i], &top, TRUE, gmx_sf);
        index_atp[i] = create_indexed_atom_type(red[i], isize[i]);
    }

    sf_table = compute_scattering_factor_table(gmx_sf, static_cast<structure_factor_t*>(sf));


    /* This is the main loop over frames */

    do
    {
        sf->nSteps++;
        for (i = 0; i < ng; i++)
        {
            rearrange_atoms(red[i], &fr, index[i], isize[i], &top, FALSE, gmx_sf);

            compute_structure_factor(static_cast<structure_factor_t*>(sf), box, red[i], isize[i],
                                     start_q, end_q, i, sf_table);
        }
    }

    while (read_next_frame(oenv, status, &fr));

    save_data(static_cast<structure_factor_t*>(sf), fnXVG, ng, start_q, end_q, oenv);


    sfree(a);
    sfree(b);

    gmx_structurefactors_done(gmx_sf);

    return 0;
}


extern void save_data(structure_factor_t*     sft,
                      const char*             file,
                      int                     ngrps,
                      real                    start_q,
                      real                    end_q,
                      const gmx_output_env_t* oenv)
{

    FILE*   fp;
    int     i, g = 0;
    double *tmp, polarization_factor, A;

    structure_factor* sf = static_cast<structure_factor*>(sft);

    fp = xvgropen(file, "Scattering Intensity", "q (1/nm)", "Intensity (a.u.)", oenv);

    snew(tmp, ngrps);

    for (g = 0; g < ngrps; g++)
    {
        for (i = 0; i < sf->n_angles; i++)
        {

            /*
             *          theta is half the angle between incoming and scattered vectors.
             *
             *          polar. fact. = 0.5*(1+cos^2(2*theta)) = 1 - 0.5 * sin^2(2*theta)
             *
             *          sin(theta) = q/(2k) := A  ->  sin^2(theta) = 4*A^2 (1-A^2) ->
             *          -> 0.5*(1+cos^2(2*theta)) = 1 - 2 A^2 (1-A^2)
             */
            A                   = static_cast<double>(i * sf->ref_k) / (2.0 * sf->momentum);
            polarization_factor = 1 - 2.0 * gmx::square(A) * (1 - gmx::square(A));
            sf->F[g][i] *= polarization_factor;
        }
    }
    for (i = 0; i < sf->n_angles; i++)
    {
        if (i * sf->ref_k >= start_q && i * sf->ref_k <= end_q)
        {
            fprintf(fp, "%10.5f  ", i * sf->ref_k);
            for (g = 0; g < ngrps; g++)
            {
                fprintf(fp, "  %10.5f ", (sf->F[g][i]) / (sf->total_n_atoms * sf->nSteps));
            }
            fprintf(fp, "\n");
        }
    }

    xvgrclose(fp);
}


extern double CMSF(gmx_structurefactors_t* gsf, int type, int nh, double lambda, double sin_theta)
/*
 * return Cromer-Mann fit for the atomic scattering factor:
 * sin_theta is the sine of half the angle between incoming and scattered
 * vectors. See g_sq.h for a short description of CM fit.
 */
{
    int    i;
    double tmp = 0.0, k2;
    real * a, *b;
    real   c;

    snew(a, 4);
    snew(b, 4);

    /*
     *
     * f0[k] = c + [SUM a_i*EXP(-b_i*(k^2)) ]
     *             i=1,4
     */

    /*
     *  united atoms case
     *  CH2 / CH3 groups
     */
    if (nh > 0)
    {
        tmp = (CMSF(gsf, return_atom_type("C", gsf), 0, lambda, sin_theta)
               + nh * CMSF(gsf, return_atom_type("H", gsf), 0, lambda, sin_theta));
    }
    /* all atom case */
    else
    {
        k2 = (gmx::square(sin_theta) / gmx::square(10.0 * lambda));
        gmx_structurefactors_get_sf(gsf, type, a, b, &c);
        tmp = c;
        for (i = 0; (i < 4); i++)
        {
            tmp += a[i] * exp(-b[i] * k2);
        }
    }
    return tmp;
}


extern real** gmx_structurefactors_table(gmx_structurefactors_t* gsf, real momentum, real ref_k, real lambda, int n_angles)
{

    int                   NCMT;
    int                   nsftable;
    int                   i, j;
    double                q, sin_theta;
    real**                sf_table;
    gmx_structurefactors* gsft = static_cast<gmx_structurefactors*>(gsf);

    NCMT     = gsft->nratoms;
    nsftable = NCMT + 3;

    snew(sf_table, nsftable);
    for (i = 0; (i < nsftable); i++)
    {
        snew(sf_table[i], n_angles);
        for (j = 0; j < n_angles; j++)
        {
            q = static_cast<double>(j * ref_k);
            /* theta is half the angle between incoming
               and scattered wavevectors. */
            sin_theta = q / (2.0 * momentum);
            if (i < NCMT)
            {
                sf_table[i][j] = CMSF(gsf, i, 0, lambda, sin_theta);
            }
            else
            {
                sf_table[i][j] = CMSF(gsf, i, i - NCMT + 1, lambda, sin_theta);
            }
        }
    }
    return sf_table;
}

extern void gmx_structurefactors_done(gmx_structurefactors_t* gsf)
{

    int                   i;
    gmx_structurefactors* sf;
    sf = static_cast<gmx_structurefactors*>(gsf);

    for (i = 0; i < sf->nratoms; i++)
    {
        sfree(sf->a[i]);
        sfree(sf->b[i]);
        sfree(sf->atomnm[i]);
    }

    sfree(sf->a);
    sfree(sf->b);
    sfree(sf->atomnm);
    sfree(sf->p);
    sfree(sf->c);

    sfree(sf);
}

extern real** compute_scattering_factor_table(gmx_structurefactors_t* gsf, structure_factor_t* sft)
{
    /*
     *  this function build up a table of scattering factors for every atom
     *  type and for every scattering angle.
     */

    double hc = 1239.842;
    real** sf_table;

    structure_factor* sf = static_cast<structure_factor*>(sft);


    /* \hbar \omega \lambda = hc = 1239.842 eV * nm */
    sf->momentum = (static_cast<double>(2. * 1000.0 * M_PI * sf->energy) / hc);
    sf->lambda   = hc / (1000.0 * sf->energy);
    fprintf(stderr, "\nwavelenght = %f nm\n", sf->lambda);

    sf_table = gmx_structurefactors_table(gsf, sf->momentum, sf->ref_k, sf->lambda, sf->n_angles);

    return sf_table;
}