src/gromacs/gmxana/gmx_gyrate.c

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