src/gromacs/gmxana/gmx_sorient.c

   1 /*
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  37 #include "config.h"
  38
  39 #include "macros.h"
  40 #include "gstat.h"
  41 #include "gromacs/math/vec.h"
  42 #include "viewit.h"
  43 #include "gromacs/pbcutil/pbc.h"
  44 #include "gromacs/topology/index.h"
  45 #include "gromacs/fileio/tpxio.h"
  46 #include "gromacs/fileio/trxio.h"
  47 #include "gmx_ana.h"
  48
  49 #include "gromacs/commandline/pargs.h"
  50 #include "gromacs/fileio/xvgr.h"
  51 #include "gromacs/pbcutil/rmpbc.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
  56                          atom_id index[], rvec xref, gmx_bool bPBC)
  57 {
  58     const real tol = 1e-4;
  59     gmx_bool   bChanged;
  60     int        m, j, ai, iter;
  61     real       mass, mtot;
  62     rvec       dx, xtest;
  63
  64     /* First simple calculation */
  65     clear_rvec(xref);
  66     mtot = 0;
  67     for (m = 0; (m < nrefat); m++)
  68     {
  69         ai   = index[m];
  70         mass = top->atoms.atom[ai].m;
  71         for (j = 0; (j < DIM); j++)
  72         {
  73             xref[j] += mass*x[ai][j];
  74         }
  75         mtot += mass;
  76     }
  77     svmul(1/mtot, xref, xref);
  78     /* Now check if any atom is more than half the box from the COM */
  79     if (bPBC)
  80     {
  81         iter = 0;
  82         do
  83         {
  84             bChanged = FALSE;
  85             for (m = 0; (m < nrefat); m++)
  86             {
  87                 ai   = index[m];
  88                 mass = top->atoms.atom[ai].m/mtot;
  89                 pbc_dx(pbc, x[ai], xref, dx);
  90                 rvec_add(xref, dx, xtest);
  91                 for (j = 0; (j < DIM); j++)
  92                 {
  93                     if (fabs(xtest[j]-x[ai][j]) > tol)
  94                     {
  95                         /* Here we have used the wrong image for contributing to the COM */
  96                         xref[j] += mass*(xtest[j]-x[ai][j]);
  97                         x[ai][j] = xtest[j];
  98                         bChanged = TRUE;
  99                     }
 100                 }
 101             }
 102             if (bChanged)
 103             {
 104                 printf("COM: %8.3f  %8.3f  %8.3f  iter = %d\n", xref[XX], xref[YY], xref[ZZ], iter);
 105             }
 106             iter++;
 107         }
 108         while (bChanged);
 109     }
 110 }
 111
 112 int gmx_sorient(int argc, char *argv[])
 113 {
 114     t_topology      top;
 115     int             ePBC = -1;
 116     char            title[STRLEN];
 117     t_trxstatus    *status;
 118     int             natoms;
 119     real            t;
 120     rvec           *xtop, *x;
 121     matrix          box;
 122
 123     FILE           *fp;
 124     int             i, j, p, sa0, sa1, sa2, n, ntot, nf, m, *hist1, *hist2, *histn, nbin1, nbin2, nrbin;
 125     real           *histi1, *histi2, invbw, invrbw;
 126     double          sum1, sum2;
 127     int            *isize, nrefgrp, nrefat;
 128     atom_id       **index;
 129     char          **grpname;
 130     real            inp, outp, two_pi, nav, normfac, rmin2, rmax2, rcut, rcut2, r2, r, mass, mtot;
 131     real            c1, c2;
 132     char            str[STRLEN];
 133     gmx_bool        bTPS;
 134     rvec            xref, dx, dxh1, dxh2, outer;
 135     gmx_rmpbc_t     gpbc = NULL;
 136     t_pbc           pbc;
 137     const char     *legr[] = {
 138         "<cos(\\8q\\4\\s1\\N)>",
 139         "<3cos\\S2\\N(\\8q\\4\\s2\\N)-1>"
 140     };
 141     const char     *legc[] = {
 142         "cos(\\8q\\4\\s1\\N)",
 143         "3cos\\S2\\N(\\8q\\4\\s2\\N)-1"
 144     };
 145
 146     const char     *desc[] = {
 147         "[THISMODULE] analyzes solvent orientation around solutes.",
 148         "It calculates two angles between the vector from one or more",
 149         "reference positions to the first atom of each solvent molecule:[PAR]",
 150         "[GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
 151         "molecule to the midpoint between atoms 2 and 3.[BR]",
 152         "[GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
 153         "same three atoms, or, when the option [TT]-v23[tt] is set, ",
 154         "the angle with the vector between atoms 2 and 3.[PAR]",
 155         "The reference can be a set of atoms or",
 156         "the center of mass of a set of atoms. The group of solvent atoms should",
 157         "consist of 3 atoms per solvent molecule.",
 158         "Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
 159         "considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
 160         "[TT]-o[tt]: distribtion of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] for rmin<=r<=rmax.[PAR]",
 161         "[TT]-no[tt]: distribution of [MATH][COS][GRK]theta[grk][SUB]2[sub][cos][math] for rmin<=r<=rmax.[PAR]",
 162         "[TT]-ro[tt]: [MATH][CHEVRON][COS][GRK]theta[grk][SUB]1[sub][cos][chevron][math] and [MATH][CHEVRON]3[COS]^2[GRK]theta[grk][SUB]2[sub][cos]-1[chevron][math] as a function of the",
 163         "distance.[PAR]",
 164         "[TT]-co[tt]: the sum over all solvent molecules within distance r",
 165         "of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] and [MATH]3[COS]^2([GRK]theta[grk][SUB]2[sub])-1[cos][math] as a function of r.[PAR]",
 166         "[TT]-rc[tt]: the distribution of the solvent molecules as a function of r"
 167     };
 168
 169     output_env_t    oenv;
 170     static gmx_bool bCom = FALSE, bVec23 = FALSE, bPBC = FALSE;
 171     static real     rmin = 0.0, rmax = 0.5, binwidth = 0.02, rbinw = 0.02;
 172     t_pargs         pa[] = {
 173         { "-com",  FALSE, etBOOL,  {&bCom},
 174           "Use the center of mass as the reference postion" },
 175         { "-v23",  FALSE, etBOOL,  {&bVec23},
 176           "Use the vector between atoms 2 and 3" },
 177         { "-rmin",  FALSE, etREAL, {&rmin}, "Minimum distance (nm)" },
 178         { "-rmax",  FALSE, etREAL, {&rmax}, "Maximum distance (nm)" },
 179         { "-cbin",  FALSE, etREAL, {&binwidth}, "Binwidth for the cosine" },
 180         { "-rbin",  FALSE, etREAL, {&rbinw}, "Binwidth for r (nm)" },
 181         { "-pbc",   FALSE, etBOOL, {&bPBC}, "Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules." }
 182     };
 183
 184     t_filenm        fnm[] = {
 185         { efTRX, NULL,  NULL,  ffREAD },
 186         { efTPS, NULL,  NULL,  ffREAD },
 187         { efNDX, NULL,  NULL,  ffOPTRD },
 188         { efXVG, NULL,  "sori.xvg",  ffWRITE },
 189         { efXVG, "-no", "snor.xvg",  ffWRITE },
 190         { efXVG, "-ro", "sord.xvg",  ffWRITE },
 191         { efXVG, "-co", "scum.xvg",  ffWRITE },
 192         { efXVG, "-rc", "scount.xvg",  ffWRITE }
 193     };
 194 #define NFILE asize(fnm)
 195
 196     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
 197                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
 198     {
 199         return 0;
 200     }
 201
 202     two_pi = 2/M_PI;
 203
 204     bTPS = (opt2bSet("-s", NFILE, fnm) || !opt2bSet("-n", NFILE, fnm) || bCom);
 205     if (bTPS)
 206     {
 207         read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box,
 208                       bCom);
 209     }
 210
 211     /* get index groups */
 212     printf("Select a group of reference particles and a solvent group:\n");
 213     snew(grpname, 2);
 214     snew(index, 2);
 215     snew(isize, 2);
 216     if (bTPS)
 217     {
 218         get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 2, isize, index, grpname);
 219     }
 220     else
 221     {
 222         get_index(NULL, ftp2fn(efNDX, NFILE, fnm), 2, isize, index, grpname);
 223     }
 224
 225     if (bCom)
 226     {
 227         nrefgrp = 1;
 228         nrefat  = isize[0];
 229     }
 230     else
 231     {
 232         nrefgrp = isize[0];
 233         nrefat  = 1;
 234     }
 235
 236     if (isize[1] % 3)
 237     {
 238         gmx_fatal(FARGS, "The number of solvent atoms (%d) is not a multiple of 3",
 239                   isize[1]);
 240     }
 241
 242     /* initialize reading trajectory:                         */
 243     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 244
 245     rmin2 = sqr(rmin);
 246     rmax2 = sqr(rmax);
 247     rcut  = 0.99*sqrt(max_cutoff2(guess_ePBC(box), box));
 248     if (rcut == 0)
 249     {
 250         rcut = 10*rmax;
 251     }
 252     rcut2 = sqr(rcut);
 253
 254     invbw = 1/binwidth;
 255     nbin1 = 1+(int)(2*invbw + 0.5);
 256     nbin2 = 1+(int)(invbw + 0.5);
 257
 258     invrbw = 1/rbinw;
 259
 260     snew(hist1, nbin1);
 261     snew(hist2, nbin2);
 262     nrbin = 1+(int)(rcut/rbinw);
 263     if (nrbin == 0)
 264     {
 265         nrbin = 1;
 266     }
 267     snew(histi1, nrbin);
 268     snew(histi2, nrbin);
 269     snew(histn, nrbin);
 270
 271     ntot = 0;
 272     nf   = 0;
 273     sum1 = 0;
 274     sum2 = 0;
 275
 276     if (bTPS)
 277     {
 278         /* make molecules whole again */
 279         gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 280     }
 281     /* start analysis of trajectory */
 282     do
 283     {
 284         if (bTPS)
 285         {
 286             /* make molecules whole again */
 287             gmx_rmpbc(gpbc, natoms, box, x);
 288         }
 289
 290         set_pbc(&pbc, ePBC, box);
 291         n    = 0;
 292         inp  = 0;
 293         outp = 0;
 294         for (p = 0; (p < nrefgrp); p++)
 295         {
 296             if (bCom)
 297             {
 298                 calc_com_pbc(nrefat, &top, x, &pbc, index[0], xref, bPBC);
 299             }
 300             else
 301             {
 302                 copy_rvec(x[index[0][p]], xref);
 303             }
 304
 305             for (m = 0; m < isize[1]; m += 3)
 306             {
 307                 sa0 = index[1][m];
 308                 sa1 = index[1][m+1];
 309                 sa2 = index[1][m+2];
 310                 range_check(sa0, 0, natoms);
 311                 range_check(sa1, 0, natoms);
 312                 range_check(sa2, 0, natoms);
 313                 pbc_dx(&pbc, x[sa0], xref, dx);
 314                 r2  = norm2(dx);
 315                 if (r2 < rcut2)
 316                 {
 317                     r = sqrt(r2);
 318                     if (!bVec23)
 319                     {
 320                         /* Determine the normal to the plain */
 321                         rvec_sub(x[sa1], x[sa0], dxh1);
 322                         rvec_sub(x[sa2], x[sa0], dxh2);
 323                         rvec_inc(dxh1, dxh2);
 324                         svmul(1/r, dx, dx);
 325                         unitv(dxh1, dxh1);
 326                         inp = iprod(dx, dxh1);
 327                         cprod(dxh1, dxh2, outer);
 328                         unitv(outer, outer);
 329                         outp = iprod(dx, outer);
 330                     }
 331                     else
 332                     {
 333                         /* Use the vector between the 2nd and 3rd atom */
 334                         rvec_sub(x[sa2], x[sa1], dxh2);
 335                         unitv(dxh2, dxh2);
 336                         outp = iprod(dx, dxh2)/r;
 337                     }
 338                     {
 339                         int ii = (int)(invrbw*r);
 340                         range_check(ii, 0, nrbin);
 341                         histi1[ii] += inp;
 342                         histi2[ii] += 3*sqr(outp) - 1;
 343                         histn[ii]++;
 344                     }
 345                     if ((r2 >= rmin2) && (r2 < rmax2))
 346                     {
 347                         int ii1 = (int)(invbw*(inp + 1));
 348                         int ii2 = (int)(invbw*fabs(outp));
 349
 350                         range_check(ii1, 0, nbin1);
 351                         range_check(ii2, 0, nbin2);
 352                         hist1[ii1]++;
 353                         hist2[ii2]++;
 354                         sum1 += inp;
 355                         sum2 += outp;
 356                         n++;
 357                     }
 358                 }
 359             }
 360         }
 361         ntot += n;
 362         nf++;
 363
 364     }
 365     while (read_next_x(oenv, status, &t, x, box));
 366
 367     /* clean up */
 368     sfree(x);
 369     close_trj(status);
 370     gmx_rmpbc_done(gpbc);
 371
 372     /* Add the bin for the exact maximum to the previous bin */
 373     hist1[nbin1-1] += hist1[nbin1];
 374     hist2[nbin2-1] += hist2[nbin2];
 375
 376     nav     = (real)ntot/(nrefgrp*nf);
 377     normfac = invbw/ntot;
 378
 379     fprintf(stderr,  "Average nr of molecules between %g and %g nm: %.1f\n",
 380             rmin, rmax, nav);
 381     if (ntot > 0)
 382     {
 383         sum1 /= ntot;
 384         sum2 /= ntot;
 385         fprintf(stderr, "Average cos(theta1)     between %g and %g nm: %6.3f\n",
 386                 rmin, rmax, sum1);
 387         fprintf(stderr, "Average 3cos2(theta2)-1 between %g and %g nm: %6.3f\n",
 388                 rmin, rmax, sum2);
 389     }
 390
 391     sprintf(str, "Solvent orientation between %g and %g nm", rmin, rmax);
 392     fp = xvgropen(opt2fn("-o", NFILE, fnm), str, "cos(\\8q\\4\\s1\\N)", "", oenv);
 393     if (output_env_get_print_xvgr_codes(oenv))
 394     {
 395         fprintf(fp, "@ subtitle \"average shell size %.1f molecules\"\n", nav);
 396     }
 397     for (i = 0; i < nbin1; i++)
 398     {
 399         fprintf(fp, "%g %g\n", (i+0.5)*binwidth-1, 2*normfac*hist1[i]);
 400     }
 401     gmx_ffclose(fp);
 402
 403     sprintf(str, "Solvent normal orientation between %g and %g nm", rmin, rmax);
 404     fp = xvgropen(opt2fn("-no", NFILE, fnm), str, "cos(\\8q\\4\\s2\\N)", "", oenv);
 405     if (output_env_get_print_xvgr_codes(oenv))
 406     {
 407         fprintf(fp, "@ subtitle \"average shell size %.1f molecules\"\n", nav);
 408     }
 409     for (i = 0; i < nbin2; i++)
 410     {
 411         fprintf(fp, "%g %g\n", (i+0.5)*binwidth, normfac*hist2[i]);
 412     }
 413     gmx_ffclose(fp);
 414
 415
 416     sprintf(str, "Solvent orientation");
 417     fp = xvgropen(opt2fn("-ro", NFILE, fnm), str, "r (nm)", "", oenv);
 418     if (output_env_get_print_xvgr_codes(oenv))
 419     {
 420         fprintf(fp, "@ subtitle \"as a function of distance\"\n");
 421     }
 422     xvgr_legend(fp, 2, legr, oenv);
 423     for (i = 0; i < nrbin; i++)
 424     {
 425         fprintf(fp, "%g %g %g\n", (i+0.5)*rbinw,
 426                 histn[i] ? histi1[i]/histn[i] : 0,
 427                 histn[i] ? histi2[i]/histn[i] : 0);
 428     }
 429     gmx_ffclose(fp);
 430
 431     sprintf(str, "Cumulative solvent orientation");
 432     fp = xvgropen(opt2fn("-co", NFILE, fnm), str, "r (nm)", "", oenv);
 433     if (output_env_get_print_xvgr_codes(oenv))
 434     {
 435         fprintf(fp, "@ subtitle \"as a function of distance\"\n");
 436     }
 437     xvgr_legend(fp, 2, legc, oenv);
 438     normfac = 1.0/(nrefgrp*nf);
 439     c1      = 0;
 440     c2      = 0;
 441     fprintf(fp, "%g %g %g\n", 0.0, c1, c2);
 442     for (i = 0; i < nrbin; i++)
 443     {
 444         c1 += histi1[i]*normfac;
 445         c2 += histi2[i]*normfac;
 446         fprintf(fp, "%g %g %g\n", (i+1)*rbinw, c1, c2);
 447     }
 448     gmx_ffclose(fp);
 449
 450     sprintf(str, "Solvent distribution");
 451     fp = xvgropen(opt2fn("-rc", NFILE, fnm), str, "r (nm)", "molecules/nm", oenv);
 452     if (output_env_get_print_xvgr_codes(oenv))
 453     {
 454         fprintf(fp, "@ subtitle \"as a function of distance\"\n");
 455     }
 456     normfac = 1.0/(rbinw*nf);
 457     for (i = 0; i < nrbin; i++)
 458     {
 459         fprintf(fp, "%g %g\n", (i+0.5)*rbinw, histn[i]*normfac);
 460     }
 461     gmx_ffclose(fp);
 462
 463     do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
 464     do_view(oenv, opt2fn("-no", NFILE, fnm), NULL);
 465     do_view(oenv, opt2fn("-ro", NFILE, fnm), "-nxy");
 466     do_view(oenv, opt2fn("-co", NFILE, fnm), "-nxy");
 467
 468     return 0;
 469 }