src/gromacs/gmxana/gmx_spatial.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 #include "gmxpre.h"
  36
  37 #include <cmath>
  38 #include <cstdlib>
  39
  40 #include "gromacs/commandline/pargs.h"
  41 #include "gromacs/fileio/confio.h"
  42 #include "gromacs/fileio/trx.h"
  43 #include "gromacs/fileio/trxio.h"
  44 #include "gromacs/gmxana/gmx_ana.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/pbcutil/pbc.h"
  47 #include "gromacs/pbcutil/rmpbc.h"
  48 #include "gromacs/topology/index.h"
  49 #include "gromacs/topology/topology.h"
  50 #include "gromacs/utility/arraysize.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/futil.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 static const double bohr = 0.529177249;  /* conversion factor to compensate for VMD plugin conversion... */
  56
  57 int gmx_spatial(int argc, char *argv[])
  58 {
  59     const char       *desc[] = {
  60         "[THISMODULE] calculates the spatial distribution function and",
  61         "outputs it in a form that can be read by VMD as Gaussian98 cube format.",
  62         "For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated",
  63         "in about 30 minutes, with most of the time dedicated to the two runs through",
  64         "[TT]trjconv[tt] that are required to center everything properly.",
  65         "This also takes a whole bunch of space (3 copies of the trajectory file).",
  66         "Still, the pictures are pretty and very informative when the fitted selection is properly made.",
  67         "3-4 atoms in a widely mobile group (like a free amino acid in solution) works",
  68         "well, or select the protein backbone in a stable folded structure to get the SDF",
  69         "of solvent and look at the time-averaged solvation shell.",
  70         "It is also possible using this program to generate the SDF based on some arbitrary",
  71         "Cartesian coordinate. To do that, simply omit the preliminary [gmx-trjconv] steps.",
  72         "",
  73         "Usage:",
  74         "",
  75         "1. Use [gmx-make_ndx] to create a group containing the atoms around which you want the SDF",
  76         "2. [TT]gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric -ur compact -pbc none[tt]",
  77         "3. [TT]gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans[tt]",
  78         "4. run [THISMODULE] on the [TT]c.tng[tt] output of step #3.",
  79         "5. Load [TT]grid.cube[tt] into VMD and view as an isosurface.",
  80         "",
  81         "[BB]Note[bb] that systems such as micelles will require [TT]gmx trjconv -pbc cluster[tt] between steps 1 and 2.",
  82         "",
  83         "Warnings",
  84         "^^^^^^^^",
  85         "",
  86         "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy.",
  87         "However, the preparatory [TT]-fit rot+trans[tt] option to [gmx-trjconv] implies that your system will be rotating",
  88         "and translating in space (in order that the selected group does not). Therefore the values that are",
  89         "returned will only be valid for some region around your central group/coordinate that has full overlap",
  90         "with system volume throughout the entire translated/rotated system over the course of the trajectory.",
  91         "It is up to the user to ensure that this is the case.",
  92         "",
  93         "Risky options",
  94         "^^^^^^^^^^^^^",
  95         "",
  96         "To reduce the amount of space and time required, you can output only the coords",
  97         "that are going to be used in the first and subsequent run through [gmx-trjconv].",
  98         "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since",
  99         "memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt]",
 100         "option value."
 101     };
 102     const char       *bugs[] = {
 103         "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected "
 104         "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins) "
 105         "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again "
 106         "with an increased [TT]-nab[tt] value."
 107     };
 108
 109     static gmx_bool   bPBC         = FALSE;
 110     static int        iIGNOREOUTER = -1;   /*Positive values may help if the surface is spikey */
 111     static gmx_bool   bCUTDOWN     = TRUE;
 112     static real       rBINWIDTH    = 0.05; /* nm */
 113     static gmx_bool   bCALCDIV     = TRUE;
 114     static int        iNAB         = 4;
 115
 116     t_pargs           pa[] = {
 117         { "-pbc",      FALSE, etBOOL, {&bPBC},
 118           "Use periodic boundary conditions for computing distances" },
 119         { "-div",      FALSE, etBOOL, {&bCALCDIV},
 120           "Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE ([TT]-nodiv[tt]) to get accurate counts per frame" },
 121         { "-ign",      FALSE, etINT, {&iIGNOREOUTER},
 122           "Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible)" },
 123         /*    { "-cut",      bCUTDOWN, etBOOL, {&bCUTDOWN},*/
 124         /*      "Display a total cube that is of minimal size" }, */
 125         { "-bin",      FALSE, etREAL, {&rBINWIDTH},
 126           "Width of the bins (nm)" },
 127         { "-nab",      FALSE, etINT, {&iNAB},
 128           "Number of additional bins to ensure proper memory allocation" }
 129     };
 130
 131     double            MINBIN[3];
 132     double            MAXBIN[3];
 133     t_topology        top;
 134     int               ePBC;
 135     t_trxframe        fr;
 136     rvec             *xtop;
 137     matrix            box, box_pbc;
 138     t_trxstatus      *status;
 139     int               flags = TRX_READ_X;
 140     t_pbc             pbc;
 141     t_atoms          *atoms;
 142     int               natoms;
 143     char             *grpnm, *grpnmp;
 144     int              *index, *indexp;
 145     int               i, nidx, nidxp;
 146     int               v;
 147     int               j, k;
 148     int            ***bin = NULL;
 149     int               nbin[3];
 150     FILE             *flp;
 151     int               x, y, z, minx, miny, minz, maxx, maxy, maxz;
 152     int               numfr, numcu;
 153     int               tot, maxval, minval;
 154     double            norm;
 155     gmx_output_env_t *oenv;
 156     gmx_rmpbc_t       gpbc = NULL;
 157
 158     t_filenm          fnm[] = {
 159         { efTPS,  NULL,  NULL, ffREAD }, /* this is for the topology */
 160         { efTRX, "-f", NULL, ffREAD },   /* and this for the trajectory */
 161         { efNDX, NULL, NULL, ffOPTRD }
 162     };
 163
 164 #define NFILE asize(fnm)
 165
 166     /* This is the routine responsible for adding default options,
 167      * calling the X/motif interface, etc. */
 168     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
 169                            NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
 170     {
 171         return 0;
 172     }
 173
 174     read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box, TRUE);
 175     sfree(xtop);
 176
 177     atoms = &(top.atoms);
 178     printf("Select group to generate SDF:\n");
 179     get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nidx, &index, &grpnm);
 180     printf("Select group to output coords (e.g. solute):\n");
 181     get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nidxp, &indexp, &grpnmp);
 182
 183     /* The first time we read data is a little special */
 184     natoms = read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, flags);
 185
 186     /* Memory Allocation */
 187     MINBIN[XX] = MAXBIN[XX] = fr.x[0][XX];
 188     MINBIN[YY] = MAXBIN[YY] = fr.x[0][YY];
 189     MINBIN[ZZ] = MAXBIN[ZZ] = fr.x[0][ZZ];
 190     for (i = 1; i < top.atoms.nr; ++i)
 191     {
 192         if (fr.x[i][XX] < MINBIN[XX])
 193         {
 194             MINBIN[XX] = fr.x[i][XX];
 195         }
 196         if (fr.x[i][XX] > MAXBIN[XX])
 197         {
 198             MAXBIN[XX] = fr.x[i][XX];
 199         }
 200         if (fr.x[i][YY] < MINBIN[YY])
 201         {
 202             MINBIN[YY] = fr.x[i][YY];
 203         }
 204         if (fr.x[i][YY] > MAXBIN[YY])
 205         {
 206             MAXBIN[YY] = fr.x[i][YY];
 207         }
 208         if (fr.x[i][ZZ] < MINBIN[ZZ])
 209         {
 210             MINBIN[ZZ] = fr.x[i][ZZ];
 211         }
 212         if (fr.x[i][ZZ] > MAXBIN[ZZ])
 213         {
 214             MAXBIN[ZZ] = fr.x[i][ZZ];
 215         }
 216     }
 217     for (i = ZZ; i >= XX; --i)
 218     {
 219         MAXBIN[i]  = (std::ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH)+iNAB)*rBINWIDTH+MINBIN[i];
 220         MINBIN[i] -= iNAB*rBINWIDTH;
 221         nbin[i]    = static_cast<int>(std::ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH));
 222     }
 223     snew(bin, nbin[XX]);
 224     for (i = 0; i < nbin[XX]; ++i)
 225     {
 226         snew(bin[i], nbin[YY]);
 227         for (j = 0; j < nbin[YY]; ++j)
 228         {
 229             snew(bin[i][j], nbin[ZZ]);
 230         }
 231     }
 232     copy_mat(box, box_pbc);
 233     numfr = 0;
 234     minx  = miny = minz = 999;
 235     maxx  = maxy = maxz = 0;
 236
 237     if (bPBC)
 238     {
 239         gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
 240     }
 241     /* This is the main loop over frames */
 242     do
 243     {
 244         /* Must init pbc every step because of pressure coupling */
 245
 246         copy_mat(box, box_pbc);
 247         if (bPBC)
 248         {
 249             gmx_rmpbc_trxfr(gpbc, &fr);
 250             set_pbc(&pbc, ePBC, box_pbc);
 251         }
 252
 253         for (i = 0; i < nidx; i++)
 254         {
 255             if (fr.x[index[i]][XX] < MINBIN[XX] || fr.x[index[i]][XX] > MAXBIN[XX] ||
 256                 fr.x[index[i]][YY] < MINBIN[YY] || fr.x[index[i]][YY] > MAXBIN[YY] ||
 257                 fr.x[index[i]][ZZ] < MINBIN[ZZ] || fr.x[index[i]][ZZ] > MAXBIN[ZZ])
 258             {
 259                 printf("There was an item outside of the allocated memory. Increase the value given with the -nab option.\n");
 260                 printf("Memory was allocated for [%f,%f,%f]\tto\t[%f,%f,%f]\n", MINBIN[XX], MINBIN[YY], MINBIN[ZZ], MAXBIN[XX], MAXBIN[YY], MAXBIN[ZZ]);
 261                 printf("Memory was required for [%f,%f,%f]\n", fr.x[index[i]][XX], fr.x[index[i]][YY], fr.x[index[i]][ZZ]);
 262                 exit(1);
 263             }
 264             x = static_cast<int>(std::ceil((fr.x[index[i]][XX]-MINBIN[XX])/rBINWIDTH));
 265             y = static_cast<int>(std::ceil((fr.x[index[i]][YY]-MINBIN[YY])/rBINWIDTH));
 266             z = static_cast<int>(std::ceil((fr.x[index[i]][ZZ]-MINBIN[ZZ])/rBINWIDTH));
 267             ++bin[x][y][z];
 268             if (x < minx)
 269             {
 270                 minx = x;
 271             }
 272             if (x > maxx)
 273             {
 274                 maxx = x;
 275             }
 276             if (y < miny)
 277             {
 278                 miny = y;
 279             }
 280             if (y > maxy)
 281             {
 282                 maxy = y;
 283             }
 284             if (z < minz)
 285             {
 286                 minz = z;
 287             }
 288             if (z > maxz)
 289             {
 290                 maxz = z;
 291             }
 292         }
 293         numfr++;
 294         /* printf("%f\t%f\t%f\n",box[XX][XX],box[YY][YY],box[ZZ][ZZ]); */
 295
 296     }
 297     while (read_next_frame(oenv, status, &fr));
 298
 299     if (bPBC)
 300     {
 301         gmx_rmpbc_done(gpbc);
 302     }
 303
 304     if (!bCUTDOWN)
 305     {
 306         minx = miny = minz = 0;
 307         maxx = nbin[XX];
 308         maxy = nbin[YY];
 309         maxz = nbin[ZZ];
 310     }
 311
 312     /* OUTPUT */
 313     flp = gmx_ffopen("grid.cube", "w");
 314     fprintf(flp, "Spatial Distribution Function\n");
 315     fprintf(flp, "test\n");
 316     fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", nidxp, (MINBIN[XX]+(minx+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);
 317     fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxx-minx+1-(2*iIGNOREOUTER), rBINWIDTH*10./bohr, 0., 0.);
 318     fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxy-miny+1-(2*iIGNOREOUTER), 0., rBINWIDTH*10./bohr, 0.);
 319     fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", maxz-minz+1-(2*iIGNOREOUTER), 0., 0., rBINWIDTH*10./bohr);
 320     for (i = 0; i < nidxp; i++)
 321     {
 322         v = 2;
 323         if (*(top.atoms.atomname[indexp[i]][0]) == 'C')
 324         {
 325             v = 6;
 326         }
 327         if (*(top.atoms.atomname[indexp[i]][0]) == 'N')
 328         {
 329             v = 7;
 330         }
 331         if (*(top.atoms.atomname[indexp[i]][0]) == 'O')
 332         {
 333             v = 8;
 334         }
 335         if (*(top.atoms.atomname[indexp[i]][0]) == 'H')
 336         {
 337             v = 1;
 338         }
 339         if (*(top.atoms.atomname[indexp[i]][0]) == 'S')
 340         {
 341             v = 16;
 342         }
 343         fprintf(flp, "%5d%12.6f%12.6f%12.6f%12.6f\n", v, 0., fr.x[indexp[i]][XX]*10.0/bohr, fr.x[indexp[i]][YY]*10.0/bohr, fr.x[indexp[i]][ZZ]*10.0/bohr);
 344     }
 345
 346     tot = 0;
 347     for (k = 0; k < nbin[XX]; k++)
 348     {
 349         if (!(k < minx || k > maxx))
 350         {
 351             continue;
 352         }
 353         for (j = 0; j < nbin[YY]; j++)
 354         {
 355             if (!(j < miny || j > maxy))
 356             {
 357                 continue;
 358             }
 359             for (i = 0; i < nbin[ZZ]; i++)
 360             {
 361                 if (!(i < minz || i > maxz))
 362                 {
 363                     continue;
 364                 }
 365                 if (bin[k][j][i] != 0)
 366                 {
 367                     printf("A bin was not empty when it should have been empty. Programming error.\n");
 368                     printf("bin[%d][%d][%d] was = %d\n", k, j, i, bin[k][j][i]);
 369                     exit(1);
 370                 }
 371             }
 372         }
 373     }
 374
 375     minval = 999;
 376     maxval = 0;
 377     for (k = 0; k < nbin[XX]; k++)
 378     {
 379         if (k < minx+iIGNOREOUTER || k > maxx-iIGNOREOUTER)
 380         {
 381             continue;
 382         }
 383         for (j = 0; j < nbin[YY]; j++)
 384         {
 385             if (j < miny+iIGNOREOUTER || j > maxy-iIGNOREOUTER)
 386             {
 387                 continue;
 388             }
 389             for (i = 0; i < nbin[ZZ]; i++)
 390             {
 391                 if (i < minz+iIGNOREOUTER || i > maxz-iIGNOREOUTER)
 392                 {
 393                     continue;
 394                 }
 395                 tot += bin[k][j][i];
 396                 if (bin[k][j][i] > maxval)
 397                 {
 398                     maxval = bin[k][j][i];
 399                 }
 400                 if (bin[k][j][i] < minval)
 401                 {
 402                     minval = bin[k][j][i];
 403                 }
 404             }
 405         }
 406     }
 407
 408     numcu = (maxx-minx+1-(2*iIGNOREOUTER))*(maxy-miny+1-(2*iIGNOREOUTER))*(maxz-minz+1-(2*iIGNOREOUTER));
 409     if (bCALCDIV)
 410     {
 411         norm = static_cast<double>(numcu*numfr)/tot;
 412     }
 413     else
 414     {
 415         norm = 1.0;
 416     }
 417
 418     for (k = 0; k < nbin[XX]; k++)
 419     {
 420         if (k < minx+iIGNOREOUTER || k > maxx-iIGNOREOUTER)
 421         {
 422             continue;
 423         }
 424         for (j = 0; j < nbin[YY]; j++)
 425         {
 426             if (j < miny+iIGNOREOUTER || j > maxy-iIGNOREOUTER)
 427             {
 428                 continue;
 429             }
 430             for (i = 0; i < nbin[ZZ]; i++)
 431             {
 432                 if (i < minz+iIGNOREOUTER || i > maxz-iIGNOREOUTER)
 433                 {
 434                     continue;
 435                 }
 436                 fprintf(flp, "%12.6f ", static_cast<double>(norm*bin[k][j][i])/numfr);
 437             }
 438             fprintf(flp, "\n");
 439         }
 440         fprintf(flp, "\n");
 441     }
 442     gmx_ffclose(flp);
 443
 444     if (bCALCDIV)
 445     {
 446         printf("Counts per frame in all %d cubes divided by %le\n", numcu, 1.0/norm);
 447         printf("Normalized data: average %le, min %le, max %le\n", 1.0, minval*norm/numfr, maxval*norm/numfr);
 448     }
 449     else
 450     {
 451         printf("grid.cube contains counts per frame in all %d cubes\n", numcu);
 452         printf("Raw data: average %le, min %le, max %le\n", 1.0/norm, static_cast<double>(minval)/numfr, static_cast<double>(maxval)/numfr);
 453     }
 454
 455     return 0;
 456 }