src/gromacs/gmxana/gmx_gyrate.cpp

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  38 #include "gmxpre.h"
  39
  40 #include <cmath>
  41 #include <cstring>
  42
  43 #include "gromacs/commandline/pargs.h"
  44 #include "gromacs/commandline/viewit.h"
  45 #include "gromacs/correlationfunctions/autocorr.h"
  46 #include "gromacs/fileio/confio.h"
  47 #include "gromacs/fileio/trxio.h"
  48 #include "gromacs/fileio/xvgr.h"
  49 #include "gromacs/gmxana/gmx_ana.h"
  50 #include "gromacs/gmxana/gstat.h"
  51 #include "gromacs/gmxana/princ.h"
  52 #include "gromacs/math/functions.h"
  53 #include "gromacs/math/utilities.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/pbcutil/rmpbc.h"
  56 #include "gromacs/topology/index.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/arraysize.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #include "gromacs/utility/futil.h"
  61 #include "gromacs/utility/smalloc.h"
  62
  63 static real calc_gyro(rvec     x[],
  64                       int      gnx,
  65                       int      index[],
  66                       t_atom   atom[],
  67                       real     tm,
  68                       rvec     gvec,
  69                       rvec     d,
  70                       gmx_bool bQ,
  71                       gmx_bool bRot,
  72                       gmx_bool bMOI,
  73                       matrix   trans)
  74 {
  75     int  i, ii, m;
  76     real gyro, dx2, m0, Itot;
  77     rvec comp;
  78
  79     if (bRot)
  80     {
  81         principal_comp(gnx, index, atom, x, trans, d);
  82         Itot = norm(d);
  83         if (bMOI)
  84         {
  85             return Itot;
  86         }
  87         for (m = 0; (m < DIM); m++)
  88         {
  89             d[m] = std::sqrt(d[m] / tm);
  90         }
  91         /* rotate_atoms(gnx,index,x,trans); */
  92     }
  93     clear_rvec(comp);
  94     for (i = 0; (i < gnx); i++)
  95     {
  96         ii = index[i];
  97         if (bQ)
  98         {
  99             m0 = std::abs(atom[ii].q);
 100         }
 101         else
 102         {
 103             m0 = atom[ii].m;
 104         }
 105         for (m = 0; (m < DIM); m++)
 106         {
 107             dx2 = x[ii][m] * x[ii][m];
 108             comp[m] += dx2 * m0;
 109         }
 110     }
 111     gyro = comp[XX] + comp[YY] + comp[ZZ];
 112
 113     for (m = 0; (m < DIM); m++)
 114     {
 115         gvec[m] = std::sqrt((gyro - comp[m]) / tm);
 116     }
 117
 118     return std::sqrt(gyro / tm);
 119 }
 120
 121 static void calc_gyro_z(rvec x[], matrix box, int gnx, const int index[], t_atom atom[], int nz, real time, FILE* out)
 122 {
 123     static dvec*   inertia = nullptr;
 124     static double* tm      = nullptr;
 125     int            i, ii, j, zi;
 126     real           zf, w, sdet, e1, e2;
 127
 128     if (inertia == nullptr)
 129     {
 130         snew(inertia, nz);
 131         snew(tm, nz);
 132     }
 133
 134     for (i = 0; i < nz; i++)
 135     {
 136         clear_dvec(inertia[i]);
 137         tm[i] = 0;
 138     }
 139
 140     for (i = 0; (i < gnx); i++)
 141     {
 142         ii = index[i];
 143         zf = nz * x[ii][ZZ] / box[ZZ][ZZ];
 144         if (zf >= nz)
 145         {
 146             zf -= nz;
 147         }
 148         if (zf < 0)
 149         {
 150             zf += nz;
 151         }
 152         for (j = 0; j < 2; j++)
 153         {
 154             zi = static_cast<int>(zf + j);
 155             if (zi == nz)
 156             {
 157                 zi = 0;
 158             }
 159             w = atom[ii].m * (1 + std::cos(M_PI * (zf - zi)));
 160             inertia[zi][0] += w * gmx::square(x[ii][YY]);
 161             inertia[zi][1] += w * gmx::square(x[ii][XX]);
 162             inertia[zi][2] -= w * x[ii][XX] * x[ii][YY];
 163             tm[zi] += w;
 164         }
 165     }
 166     fprintf(out, "%10g", time);
 167     for (j = 0; j < nz; j++)
 168     {
 169         for (i = 0; i < 3; i++)
 170         {
 171             inertia[j][i] /= tm[j];
 172         }
 173         sdet = std::sqrt(gmx::square(inertia[j][0] - inertia[j][1]) + 4 * gmx::square(inertia[j][2]));
 174         e1   = std::sqrt(0.5 * (inertia[j][0] + inertia[j][1] + sdet));
 175         e2   = std::sqrt(0.5 * (inertia[j][0] + inertia[j][1] - sdet));
 176         fprintf(out, " %5.3f %5.3f", e1, e2);
 177     }
 178     fprintf(out, "\n");
 179 }
 180
 181
 182 int gmx_gyrate(int argc, char* argv[])
 183 {
 184     const char* desc[] = {
 185         "[THISMODULE] computes the radius of gyration of a molecule",
 186         "and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
 187         "as a function of time. The atoms are explicitly mass weighted.[PAR]",
 188         "The axis components corresponds to the mass-weighted root-mean-square",
 189         "of the radii components orthogonal to each axis, for example:[PAR]",
 190         "Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).[PAR]",
 191         "With the [TT]-nmol[tt] option the radius of gyration will be calculated",
 192         "for multiple molecules by splitting the analysis group in equally",
 193         "sized parts.[PAR]",
 194         "With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
 195         "of slices along the [IT]z[it]-axis are calculated."
 196     };
 197     static int      nmol = 1, nz = 0;
 198     static gmx_bool bQ = FALSE, bRot = FALSE, bMOI = FALSE;
 199     t_pargs         pa[] = {
 200         { "-nmol", FALSE, etINT, { &nmol }, "The number of molecules to analyze" },
 201         { "-q",
 202           FALSE,
 203           etBOOL,
 204           { &bQ },
 205           "Use absolute value of the charge of an atom as weighting factor instead of mass" },
 206         { "-p",
 207           FALSE,
 208           etBOOL,
 209           { &bRot },
 210           "Calculate the radii of gyration about the principal axes." },
 211         { "-moi",
 212           FALSE,
 213           etBOOL,
 214           { &bMOI },
 215           "Calculate the moments of inertia (defined by the principal axes)." },
 216         { "-nz",
 217           FALSE,
 218           etINT,
 219           { &nz },
 220           "Calculate the 2D radii of gyration of this number of slices along the z-axis" },
 221     };
 222     FILE*             out;
 223     t_trxstatus*      status;
 224     t_topology        top;
 225     PbcType           pbcType;
 226     rvec *            x, *x_s;
 227     rvec              xcm, gvec, gvec1;
 228     matrix            box, trans;
 229     gmx_bool          bACF;
 230     real**            moi_trans = nullptr;
 231     int               max_moi = 0, delta_moi = 100;
 232     rvec              d, d1; /* eigenvalues of inertia tensor */
 233     real              t, t0, tm, gyro;
 234     int               natoms;
 235     char*             grpname;
 236     int               j, m, gnx, nam, mol;
 237     int*              index;
 238     gmx_output_env_t* oenv;
 239     gmx_rmpbc_t       gpbc   = nullptr;
 240     const char*       leg[]  = { "Rg", "Rg\\sX\\N", "Rg\\sY\\N", "Rg\\sZ\\N" };
 241     const char*       legI[] = { "Itot", "I1", "I2", "I3" };
 242 #define NLEG asize(leg)
 243     t_filenm fnm[] = {
 244         { efTRX, "-f", nullptr, ffREAD },      { efTPS, nullptr, nullptr, ffREAD },
 245         { efNDX, nullptr, nullptr, ffOPTRD },  { efXVG, nullptr, "gyrate", ffWRITE },
 246         { efXVG, "-acf", "moi-acf", ffOPTWR },
 247     };
 248 #define NFILE asize(fnm)
 249     int      npargs;
 250     t_pargs* ppa;
 251
 252     npargs = asize(pa);
 253     ppa    = add_acf_pargs(&npargs, pa);
 254
 255     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa,
 256                            asize(desc), desc, 0, nullptr, &oenv))
 257     {
 258         sfree(ppa);
 259         return 0;
 260     }
 261     bACF = opt2bSet("-acf", NFILE, fnm);
 262     if (bACF && nmol != 1)
 263     {
 264         gmx_fatal(FARGS, "Can only do acf with nmol=1");
 265     }
 266     bRot = bRot || bMOI || bACF;
 267     /*
 268        if (nz > 0)
 269        bMOI = TRUE;
 270      */
 271     if (bRot)
 272     {
 273         printf("Will rotate system along principal axes\n");
 274         snew(moi_trans, DIM);
 275     }
 276     if (bMOI)
 277     {
 278         printf("Will print moments of inertia\n");
 279         bQ = FALSE;
 280     }
 281     if (bQ)
 282     {
 283         printf("Will print radius normalised by charge\n");
 284     }
 285
 286     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &x, nullptr, box, TRUE);
 287     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 288
 289     if (nmol > gnx || gnx % nmol != 0)
 290     {
 291         gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
 292     }
 293     nam = gnx / nmol;
 294
 295     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 296     snew(x_s, natoms);
 297
 298     j  = 0;
 299     t0 = t;
 300     if (bQ)
 301     {
 302         out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Radius of Charge (total and around axes)",
 303                        "Time (ps)", "Rg (nm)", oenv);
 304     }
 305     else if (bMOI)
 306     {
 307         out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Moments of inertia (total and around axes)",
 308                        "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
 309     }
 310     else
 311     {
 312         out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Radius of gyration (total and around axes)",
 313                        "Time (ps)", "Rg (nm)", oenv);
 314     }
 315     if (bMOI)
 316     {
 317         xvgr_legend(out, NLEG, legI, oenv);
 318     }
 319     else
 320     {
 321         if (bRot)
 322         {
 323             if (output_env_get_print_xvgr_codes(oenv))
 324             {
 325                 fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
 326             }
 327         }
 328         xvgr_legend(out, NLEG, leg, oenv);
 329     }
 330     if (nz == 0)
 331     {
 332         gpbc = gmx_rmpbc_init(&top.idef, pbcType, natoms);
 333     }
 334     do
 335     {
 336         if (nz == 0)
 337         {
 338             gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
 339         }
 340         gyro = 0;
 341         clear_rvec(gvec);
 342         clear_rvec(gvec1);
 343         clear_rvec(d);
 344         clear_rvec(d1);
 345         for (mol = 0; mol < nmol; mol++)
 346         {
 347             tm = sub_xcm(nz == 0 ? x_s : x, nam, index + mol * nam, top.atoms.atom, xcm, bQ);
 348             if (nz == 0)
 349             {
 350                 gyro += calc_gyro(x_s, nam, index + mol * nam, top.atoms.atom, tm, gvec1, d1, bQ,
 351                                   bRot, bMOI, trans);
 352             }
 353             else
 354             {
 355                 calc_gyro_z(x, box, nam, index + mol * nam, top.atoms.atom, nz, t, out);
 356             }
 357             rvec_inc(gvec, gvec1);
 358             rvec_inc(d, d1);
 359         }
 360         if (nmol > 0)
 361         {
 362             gyro /= nmol;
 363             svmul(1.0 / nmol, gvec, gvec);
 364             svmul(1.0 / nmol, d, d);
 365         }
 366
 367         if (nz == 0)
 368         {
 369             if (bRot)
 370             {
 371                 if (j >= max_moi)
 372                 {
 373                     max_moi += delta_moi;
 374                     for (m = 0; (m < DIM); m++)
 375                     {
 376                         srenew(moi_trans[m], max_moi * DIM);
 377                     }
 378                 }
 379                 for (m = 0; (m < DIM); m++)
 380                 {
 381                     copy_rvec(trans[m], moi_trans[m] + DIM * j);
 382                 }
 383                 fprintf(out, "%10g  %10g  %10g  %10g  %10g\n", t, gyro, d[XX], d[YY], d[ZZ]);
 384             }
 385             else
 386             {
 387                 fprintf(out, "%10g  %10g  %10g  %10g  %10g\n", t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
 388             }
 389         }
 390         j++;
 391     } while (read_next_x(oenv, status, &t, x, box));
 392     close_trx(status);
 393     if (nz == 0)
 394     {
 395         gmx_rmpbc_done(gpbc);
 396     }
 397
 398     xvgrclose(out);
 399
 400     if (bACF)
 401     {
 402         int mode = eacVector;
 403
 404         do_autocorr(opt2fn("-acf", NFILE, fnm), oenv, "Moment of inertia vector ACF", j, 3,
 405                     moi_trans, (t - t0) / j, mode, FALSE);
 406         do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
 407     }
 408
 409     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
 410
 411     return 0;
 412 }