src/gromacs/gmxana/gmx_gyrate.c

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  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <math.h>
  42 #include <string.h>
  43
  44 #include "gromacs/commandline/pargs.h"
  45 #include "typedefs.h"
  46 #include "gromacs/utility/smalloc.h"
  47 #include "macros.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/utility/futil.h"
  50 #include "index.h"
  51 #include "gromacs/fileio/xvgr.h"
  52 #include "viewit.h"
  53 #include "princ.h"
  54 #include "gromacs/pbcutil/rmpbc.h"
  55 #include "txtdump.h"
  56 #include "gromacs/fileio/tpxio.h"
  57 #include "gromacs/fileio/trxio.h"
  58 #include "gstat.h"
  59 #include "gmx_ana.h"
  60
  61 #include "gromacs/utility/fatalerror.h"
  62
  63 real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
  64                rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
  65 {
  66     int    i, ii, m;
  67     real   gyro, dx2, m0, Itot;
  68     rvec   comp;
  69
  70     if (bRot)
  71     {
  72         principal_comp(gnx, index, atom, x, trans, d);
  73         Itot = norm(d);
  74         if (bMOI)
  75         {
  76             return Itot;
  77         }
  78         for (m = 0; (m < DIM); m++)
  79         {
  80             d[m] = sqrt(d[m]/tm);
  81         }
  82 #ifdef DEBUG
  83         pr_rvecs(stderr, 0, "trans", trans, DIM);
  84 #endif
  85         /* rotate_atoms(gnx,index,x,trans); */
  86     }
  87     clear_rvec(comp);
  88     for (i = 0; (i < gnx); i++)
  89     {
  90         ii = index[i];
  91         if (bQ)
  92         {
  93             m0 = fabs(atom[ii].q);
  94         }
  95         else
  96         {
  97             m0 = atom[ii].m;
  98         }
  99         for (m = 0; (m < DIM); m++)
 100         {
 101             dx2      = x[ii][m]*x[ii][m];
 102             comp[m] += dx2*m0;
 103         }
 104     }
 105     gyro = comp[XX]+comp[YY]+comp[ZZ];
 106
 107     for (m = 0; (m < DIM); m++)
 108     {
 109         gvec[m] = sqrt((gyro-comp[m])/tm);
 110     }
 111
 112     return sqrt(gyro/tm);
 113 }
 114
 115 void calc_gyro_z(rvec x[], matrix box,
 116                  int gnx, atom_id index[], t_atom atom[],
 117                  int nz, real time, FILE *out)
 118 {
 119     static dvec   *inertia = NULL;
 120     static double *tm      = NULL;
 121     int            i, ii, j, zi;
 122     real           zf, w, sdet, e1, e2;
 123
 124     if (inertia == NULL)
 125     {
 126         snew(inertia, nz);
 127         snew(tm, nz);
 128     }
 129
 130     for (i = 0; i < nz; i++)
 131     {
 132         clear_dvec(inertia[i]);
 133         tm[i] = 0;
 134     }
 135
 136     for (i = 0; (i < gnx); i++)
 137     {
 138         ii = index[i];
 139         zf = nz*x[ii][ZZ]/box[ZZ][ZZ];
 140         if (zf >= nz)
 141         {
 142             zf -= nz;
 143         }
 144         if (zf < 0)
 145         {
 146             zf += nz;
 147         }
 148         for (j = 0; j < 2; j++)
 149         {
 150             zi = zf + j;
 151             if (zi == nz)
 152             {
 153                 zi = 0;
 154             }
 155             w               = atom[ii].m*(1 + cos(M_PI*(zf - zi)));
 156             inertia[zi][0] += w*sqr(x[ii][YY]);
 157             inertia[zi][1] += w*sqr(x[ii][XX]);
 158             inertia[zi][2] -= w*x[ii][XX]*x[ii][YY];
 159             tm[zi]         += w;
 160         }
 161     }
 162     fprintf(out, "%10g", time);
 163     for (j = 0; j < nz; j++)
 164     {
 165         for (i = 0; i < 3; i++)
 166         {
 167             inertia[j][i] /= tm[j];
 168         }
 169         sdet = sqrt(sqr(inertia[j][0] - inertia[j][1]) + 4*sqr(inertia[j][2]));
 170         e1   = sqrt(0.5*(inertia[j][0] + inertia[j][1] + sdet));
 171         e2   = sqrt(0.5*(inertia[j][0] + inertia[j][1] - sdet));
 172         fprintf(out, " %5.3f %5.3f", e1, e2);
 173     }
 174     fprintf(out, "\n");
 175 }
 176
 177 int gmx_gyrate(int argc, char *argv[])
 178 {
 179     const char     *desc[] = {
 180         "[THISMODULE] computes the radius of gyration of a molecule",
 181         "and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
 182         "as a function of time. The atoms are explicitly mass weighted.[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 = NULL;
 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, title[256];
 217     int             i, j, m, gnx, nam, mol;
 218     atom_id        *index;
 219     output_env_t    oenv;
 220     gmx_rmpbc_t     gpbc   = NULL;
 221     const char     *leg[]  = { "Rg", "RgX", "RgY", "RgZ" };
 222     const char     *legI[] = { "Itot", "I1", "I2", "I3" };
 223 #define NLEG asize(leg)
 224     t_filenm        fnm[] = {
 225         { efTRX, "-f",   NULL,       ffREAD },
 226         { efTPS, NULL,   NULL,       ffREAD },
 227         { efNDX, NULL,   NULL,       ffOPTRD },
 228         { efXVG, NULL,   "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 | PCA_BE_NICE,
 239                            NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
 240     {
 241         return 0;
 242     }
 243     bACF = opt2bSet("-acf", NFILE, fnm);
 244     if (bACF && nmol != 1)
 245     {
 246         gmx_fatal(FARGS, "Can only do acf with nmol=1");
 247     }
 248     bRot = bRot || bMOI || bACF;
 249     /*
 250        if (nz > 0)
 251        bMOI = TRUE;
 252      */
 253     if (bRot)
 254     {
 255         printf("Will rotate system along principal axes\n");
 256         snew(moi_trans, DIM);
 257     }
 258     if (bMOI)
 259     {
 260         printf("Will print moments of inertia\n");
 261         bQ = FALSE;
 262     }
 263     if (bQ)
 264     {
 265         printf("Will print radius normalised by charge\n");
 266     }
 267
 268     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
 269     get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 270
 271     if (nmol > gnx || gnx % nmol != 0)
 272     {
 273         gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
 274     }
 275     nam = gnx/nmol;
 276
 277     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 278     snew(x_s, natoms);
 279
 280     j  = 0;
 281     t0 = t;
 282     if (bQ)
 283     {
 284         out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 285                        "Radius of Charge", "Time (ps)", "Rg (nm)", oenv);
 286     }
 287     else if (bMOI)
 288     {
 289         out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 290                        "Moments of inertia", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
 291     }
 292     else
 293     {
 294         out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
 295                        "Radius of gyration", "Time (ps)", "Rg (nm)", oenv);
 296     }
 297     if (bMOI)
 298     {
 299         xvgr_legend(out, NLEG, legI, oenv);
 300     }
 301     else
 302     {
 303         if (bRot)
 304         {
 305             if (output_env_get_print_xvgr_codes(oenv))
 306             {
 307                 fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
 308             }
 309         }
 310         xvgr_legend(out, NLEG, leg, oenv);
 311     }
 312     if (nz == 0)
 313     {
 314         gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 315     }
 316     do
 317     {
 318         if (nz == 0)
 319         {
 320             gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
 321         }
 322         gyro = 0;
 323         clear_rvec(gvec);
 324         clear_rvec(d);
 325         for (mol = 0; mol < nmol; mol++)
 326         {
 327             tm    = sub_xcm(nz == 0 ? x_s : x, nam, index+mol*nam, top.atoms.atom, xcm, bQ);
 328             if (nz == 0)
 329             {
 330                 gyro += calc_gyro(x_s, nam, index+mol*nam, top.atoms.atom,
 331                                   tm, gvec1, d1, bQ, bRot, bMOI, trans);
 332             }
 333             else
 334             {
 335                 calc_gyro_z(x, box, nam, index+mol*nam, top.atoms.atom, nz, t, out);
 336             }
 337             rvec_inc(gvec, gvec1);
 338             rvec_inc(d, d1);
 339         }
 340         if (nmol > 0)
 341         {
 342             gyro /= nmol;
 343             svmul(1.0/nmol, gvec, gvec);
 344             svmul(1.0/nmol, d, d);
 345         }
 346
 347         if (nz == 0)
 348         {
 349             if (bRot)
 350             {
 351                 if (j >= max_moi)
 352                 {
 353                     max_moi += delta_moi;
 354                     for (m = 0; (m < DIM); m++)
 355                     {
 356                         srenew(moi_trans[m], max_moi*DIM);
 357                     }
 358                 }
 359                 for (m = 0; (m < DIM); m++)
 360                 {
 361                     copy_rvec(trans[m], moi_trans[m]+DIM*j);
 362                 }
 363                 fprintf(out, "%10g  %10g  %10g  %10g  %10g\n",
 364                         t, gyro, d[XX], d[YY], d[ZZ]);
 365             }
 366             else
 367             {
 368                 fprintf(out, "%10g  %10g  %10g  %10g  %10g\n",
 369                         t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
 370             }
 371         }
 372         j++;
 373     }
 374     while (read_next_x(oenv, status, &t, x, box));
 375     close_trj(status);
 376     if (nz == 0)
 377     {
 378         gmx_rmpbc_done(gpbc);
 379     }
 380
 381     gmx_ffclose(out);
 382
 383     if (bACF)
 384     {
 385         int mode = eacVector;
 386
 387         do_autocorr(opt2fn("-acf", NFILE, fnm), oenv,
 388                     "Moment of inertia vector ACF",
 389                     j, 3, moi_trans, (t-t0)/j, mode, FALSE);
 390         do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
 391     }
 392
 393     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
 394
 395     return 0;
 396 }