src/gromacs/gmxana/gmx_gyrate.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/commandline/viewit.h"
  44 #include "gromacs/correlationfunctions/autocorr.h"
  45 #include "gromacs/fileio/confio.h"
  46 #include "gromacs/fileio/trxio.h"
  47 #include "gromacs/fileio/xvgr.h"
  48 #include "gromacs/gmxana/gmx_ana.h"
  49 #include "gromacs/gmxana/gstat.h"
  50 #include "gromacs/gmxana/princ.h"
  51 #include "gromacs/math/functions.h"
  52 #include "gromacs/math/utilities.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/pbcutil/rmpbc.h"
  55 #include "gromacs/topology/index.h"
  56 #include "gromacs/topology/topology.h"
  57 #include "gromacs/utility/arraysize.h"
  58 #include "gromacs/utility/fatalerror.h"
  59 #include "gromacs/utility/futil.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 static real calc_gyro(rvec x[], int gnx, int index[], t_atom atom[], real tm,
  63                       rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
  64 {
  65     int    i, ii, m;
  66     real   gyro, dx2, m0, Itot;
  67     rvec   comp;
  68
  69     if (bRot)
  70     {
  71         principal_comp(gnx, index, atom, x, trans, d);
  72         Itot = norm(d);
  73         if (bMOI)
  74         {
  75             return Itot;
  76         }
  77         for (m = 0; (m < DIM); m++)
  78         {
  79             d[m] = std::sqrt(d[m]/tm);
  80         }
  81         /* rotate_atoms(gnx,index,x,trans); */
  82     }
  83     clear_rvec(comp);
  84     for (i = 0; (i < gnx); i++)
  85     {
  86         ii = index[i];
  87         if (bQ)
  88         {
  89             m0 = std::abs(atom[ii].q);
  90         }
  91         else
  92         {
  93             m0 = atom[ii].m;
  94         }
  95         for (m = 0; (m < DIM); m++)
  96         {
  97             dx2      = x[ii][m]*x[ii][m];
  98             comp[m] += dx2*m0;
  99         }
 100     }
 101     gyro = comp[XX]+comp[YY]+comp[ZZ];
 102
 103     for (m = 0; (m < DIM); m++)
 104     {
 105         gvec[m] = std::sqrt((gyro-comp[m])/tm);
 106     }
 107
 108     return std::sqrt(gyro/tm);
 109 }
 110
 111 static void calc_gyro_z(rvec x[], matrix box,
 112                         int gnx, const int index[], t_atom atom[],
 113                         int nz, real time, FILE *out)
 114 {
 115     static dvec   *inertia = nullptr;
 116     static double *tm      = nullptr;
 117     int            i, ii, j, zi;
 118     real           zf, w, sdet, e1, e2;
 119
 120     if (inertia == nullptr)
 121     {
 122         snew(inertia, nz);
 123         snew(tm, nz);
 124     }
 125
 126     for (i = 0; i < nz; i++)
 127     {
 128         clear_dvec(inertia[i]);
 129         tm[i] = 0;
 130     }
 131
 132     for (i = 0; (i < gnx); i++)
 133     {
 134         ii = index[i];
 135         zf = nz*x[ii][ZZ]/box[ZZ][ZZ];
 136         if (zf >= nz)
 137         {
 138             zf -= nz;
 139         }
 140         if (zf < 0)
 141         {
 142             zf += nz;
 143         }
 144         for (j = 0; j < 2; j++)
 145         {
 146             zi = static_cast<int>(zf + j);
 147             if (zi == nz)
 148             {
 149                 zi = 0;
 150             }
 151             w               = atom[ii].m*(1 + std::cos(M_PI*(zf - zi)));
 152             inertia[zi][0] += w*gmx::square(x[ii][YY]);
 153             inertia[zi][1] += w*gmx::square(x[ii][XX]);
 154             inertia[zi][2] -= w*x[ii][XX]*x[ii][YY];
 155             tm[zi]         += w;
 156         }
 157     }
 158     fprintf(out, "%10g", time);
 159     for (j = 0; j < nz; j++)
 160     {
 161         for (i = 0; i < 3; i++)
 162         {
 163             inertia[j][i] /= tm[j];
 164         }
 165         sdet = std::sqrt(gmx::square(inertia[j][0] - inertia[j][1]) + 4*gmx::square(inertia[j][2]));
 166         e1   = std::sqrt(0.5*(inertia[j][0] + inertia[j][1] + sdet));
 167         e2   = std::sqrt(0.5*(inertia[j][0] + inertia[j][1] - sdet));
 168         fprintf(out, " %5.3f %5.3f", e1, e2);
 169     }
 170     fprintf(out, "\n");
 171 }
 172
 173
 174 int gmx_gyrate(int argc, char *argv[])
 175 {
 176     const char       *desc[] = {
 177         "[THISMODULE] computes the radius of gyration of a molecule",
 178         "and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
 179         "as a function of time. The atoms are explicitly mass weighted.[PAR]",
 180         "The axis components corresponds to the mass-weighted root-mean-square",
 181         "of the radii components orthogonal to each axis, for example:[PAR]",
 182         "Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).[PAR]",
 183         "With the [TT]-nmol[tt] option the radius of gyration will be calculated",
 184         "for multiple molecules by splitting the analysis group in equally",
 185         "sized parts.[PAR]",
 186         "With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
 187         "of slices along the [IT]z[it]-axis are calculated."
 188     };
 189     static int        nmol = 1, nz = 0;
 190     static gmx_bool   bQ   = FALSE, bRot = FALSE, bMOI = FALSE;
 191     t_pargs           pa[] = {
 192         { "-nmol", FALSE, etINT, {&nmol},
 193           "The number of molecules to analyze" },
 194         { "-q", FALSE, etBOOL, {&bQ},
 195           "Use absolute value of the charge of an atom as weighting factor instead of mass" },
 196         { "-p", FALSE, etBOOL, {&bRot},
 197           "Calculate the radii of gyration about the principal axes." },
 198         { "-moi", FALSE, etBOOL, {&bMOI},
 199           "Calculate the moments of inertia (defined by the principal axes)." },
 200         { "-nz", FALSE, etINT, {&nz},
 201           "Calculate the 2D radii of gyration of this number of slices along the z-axis" },
 202     };
 203     FILE             *out;
 204     t_trxstatus      *status;
 205     t_topology        top;
 206     int               ePBC;
 207     rvec             *x, *x_s;
 208     rvec              xcm, gvec, gvec1;
 209     matrix            box, trans;
 210     gmx_bool          bACF;
 211     real            **moi_trans = nullptr;
 212     int               max_moi   = 0, delta_moi = 100;
 213     rvec              d, d1; /* eigenvalues of inertia tensor */
 214     real              t, t0, tm, gyro;
 215     int               natoms;
 216     char             *grpname;
 217     int               j, m, gnx, nam, mol;
 218     int              *index;
 219     gmx_output_env_t *oenv;
 220     gmx_rmpbc_t       gpbc   = nullptr;
 221     const char       *leg[]  = { "Rg", "Rg\\sX\\N", "Rg\\sY\\N", "Rg\\sZ\\N" };
 222     const char       *legI[] = { "Itot", "I1", "I2", "I3" };
 223 #define NLEG asize(leg)
 224     t_filenm          fnm[] = {
 225         { efTRX, "-f",   nullptr,       ffREAD },
 226         { efTPS, nullptr,   nullptr,       ffREAD },
 227         { efNDX, nullptr,   nullptr,       ffOPTRD },
 228         { efXVG, nullptr,   "gyrate",   ffWRITE },
 229         { efXVG, "-acf", "moi-acf",  ffOPTWR },
 230     };
 231 #define NFILE asize(fnm)
 232     int               npargs;
 233     t_pargs          *ppa;
 234
 235     npargs = asize(pa);
 236     ppa    = add_acf_pargs(&npargs, pa);
 237
 238     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
 239                            NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
 240     {
 241         sfree(ppa);
 242         return 0;
 243     }
 244     bACF = opt2bSet("-acf", NFILE, fnm);
 245     if (bACF && nmol != 1)
 246     {
 247         gmx_fatal(FARGS, "Can only do acf with nmol=1");
 248     }
 249     bRot = bRot || bMOI || bACF;
 250     /*
 251        if (nz > 0)
 252        bMOI = TRUE;
 253      */
 254     if (bRot)
 255     {
 256         printf("Will rotate system along principal axes\n");
 257         snew(moi_trans, DIM);
 258     }
 259     if (bMOI)
 260     {
 261         printf("Will print moments of inertia\n");
 262         bQ = FALSE;
 263     }
 264     if (bQ)
 265     {
 266         printf("Will print radius normalised by charge\n");
 267     }
 268
 269     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box, TRUE);
 270     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 271
 272     if (nmol > gnx || gnx % nmol != 0)
 273     {
 274         gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
 275     }
 276     nam = gnx/nmol;
 277
 278     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 279     snew(x_s, natoms);
 280
 281     j  = 0;
 282     t0 = t;
 283     if (bQ)
 284     {
 285         out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 286                        "Radius of Charge (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
 287     }
 288     else if (bMOI)
 289     {
 290         out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 291                        "Moments of inertia (total and around axes)", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
 292     }
 293     else
 294     {
 295         out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 296                        "Radius of gyration (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
 297     }
 298     if (bMOI)
 299     {
 300         xvgr_legend(out, NLEG, legI, oenv);
 301     }
 302     else
 303     {
 304         if (bRot)
 305         {
 306             if (output_env_get_print_xvgr_codes(oenv))
 307             {
 308                 fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
 309             }
 310         }
 311         xvgr_legend(out, NLEG, leg, oenv);
 312     }
 313     if (nz == 0)
 314     {
 315         gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 316     }
 317     do
 318     {
 319         if (nz == 0)
 320         {
 321             gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
 322         }
 323         gyro = 0;
 324         clear_rvec(gvec);
 325         clear_rvec(gvec1);
 326         clear_rvec(d);
 327         clear_rvec(d1);
 328         for (mol = 0; mol < nmol; mol++)
 329         {
 330             tm    = sub_xcm(nz == 0 ? x_s : x, nam, index+mol*nam, top.atoms.atom, xcm, bQ);
 331             if (nz == 0)
 332             {
 333                 gyro += calc_gyro(x_s, nam, index+mol*nam, top.atoms.atom,
 334                                   tm, gvec1, d1, bQ, bRot, bMOI, trans);
 335             }
 336             else
 337             {
 338                 calc_gyro_z(x, box, nam, index+mol*nam, top.atoms.atom, nz, t, out);
 339             }
 340             rvec_inc(gvec, gvec1);
 341             rvec_inc(d, d1);
 342         }
 343         if (nmol > 0)
 344         {
 345             gyro /= nmol;
 346             svmul(1.0/nmol, gvec, gvec);
 347             svmul(1.0/nmol, d, d);
 348         }
 349
 350         if (nz == 0)
 351         {
 352             if (bRot)
 353             {
 354                 if (j >= max_moi)
 355                 {
 356                     max_moi += delta_moi;
 357                     for (m = 0; (m < DIM); m++)
 358                     {
 359                         srenew(moi_trans[m], max_moi*DIM);
 360                     }
 361                 }
 362                 for (m = 0; (m < DIM); m++)
 363                 {
 364                     copy_rvec(trans[m], moi_trans[m]+DIM*j);
 365                 }
 366                 fprintf(out, "%10g  %10g  %10g  %10g  %10g\n",
 367                         t, gyro, d[XX], d[YY], d[ZZ]);
 368             }
 369             else
 370             {
 371                 fprintf(out, "%10g  %10g  %10g  %10g  %10g\n",
 372                         t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
 373             }
 374         }
 375         j++;
 376     }
 377     while (read_next_x(oenv, status, &t, x, box));
 378     close_trx(status);
 379     if (nz == 0)
 380     {
 381         gmx_rmpbc_done(gpbc);
 382     }
 383
 384     xvgrclose(out);
 385
 386     if (bACF)
 387     {
 388         int mode = eacVector;
 389
 390         do_autocorr(opt2fn("-acf", NFILE, fnm), oenv,
 391                     "Moment of inertia vector ACF",
 392                     j, 3, moi_trans, (t-t0)/j, mode, FALSE);
 393         do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
 394     }
 395
 396     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
 397
 398     return 0;
 399 }