src/tools/gmx_h2order.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40
  41 #include "sysstuff.h"
  42 #include <string.h>
  43 #include "typedefs.h"
  44 #include "smalloc.h"
  45 #include "macros.h"
  46 #include "princ.h"
  47 #include "rmpbc.h"
  48 #include "vec.h"
  49 #include "xvgr.h"
  50 #include "pbc.h"
  51 #include "copyrite.h"
  52 #include "futil.h"
  53 #include "statutil.h"
  54 #include "index.h"
  55 #include "gmx_ana.h"
  56
  57
  58 /****************************************************************************/
  59 /* This program calculates the ordering of water molecules across a box, as */
  60 /* function of the z-coordinate. This implies averaging over slices and over*/
  61 /* time. Output is the average cos of the angle of the dipole with the      */
  62 /* normal, per slice.                                                       */
  63 /* In addition, it calculates the average dipole moment itself in three     */
  64 /* directions.                                                              */
  65 /****************************************************************************/
  66
  67 void calc_h2order(const char *fn, atom_id index[], int ngx, rvec **slDipole,
  68                   real **slOrder, real *slWidth, int *nslices,
  69                   t_topology *top, int ePBC,
  70                   int axis, gmx_bool bMicel, atom_id micel[], int nmic,
  71                   const output_env_t oenv)
  72 {
  73     rvec *x0,            /* coordinates with pbc */
  74           dipole,        /* dipole moment due to one molecules */
  75           normal,
  76           com;           /* center of mass of micel, with bMicel */
  77     rvec        *dip;    /* sum of dipoles, unnormalized */
  78     matrix       box;    /* box (3x3) */
  79     t_trxstatus *status;
  80     real         t,      /* time from trajectory */
  81     *sum,                /* sum of all cosines of dipoles, per slice */
  82     *frame;              /* order over one frame */
  83     int natoms,          /* nr. atoms in trj */
  84         i, j, teller = 0,
  85         slice = 0,       /* current slice number */
  86     *count;              /* nr. of atoms in one slice */
  87     gmx_rmpbc_t  gpbc = NULL;
  88
  89     if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
  90     {
  91         gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
  92     }
  93
  94     if (!*nslices)
  95     {
  96         *nslices = (int)(box[axis][axis] * 10); /* default value */
  97
  98
  99     }
 100     switch (axis)
 101     {
 102         case 0:
 103             normal[0] = 1; normal[1] = 0; normal[2] = 0;
 104             break;
 105         case 1:
 106             normal[0] = 0; normal[1] = 1; normal[2] = 0;
 107             break;
 108         case 2:
 109             normal[0] = 0; normal[1] = 0; normal[2] = 1;
 110             break;
 111         default:
 112             gmx_fatal(FARGS, "No valid value for -axis-. Exiting.\n");
 113             /* make compiler happy */
 114             normal[0] = 1; normal[1] = 0; normal[2] = 0;
 115     }
 116
 117     clear_rvec(dipole);
 118     snew(count, *nslices);
 119     snew(sum, *nslices);
 120     snew(dip, *nslices);
 121     snew(frame, *nslices);
 122
 123     *slWidth = box[axis][axis]/(*nslices);
 124     fprintf(stderr, "Box divided in %d slices. Initial width of slice: %f\n",
 125             *nslices, *slWidth);
 126
 127     teller = 0;
 128
 129     gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms, box);
 130     /*********** Start processing trajectory ***********/
 131     do
 132     {
 133         *slWidth = box[axis][axis]/(*nslices);
 134         teller++;
 135
 136         gmx_rmpbc(gpbc, natoms, box, x0);
 137
 138         if (bMicel)
 139         {
 140             calc_xcm(x0, nmic, micel, top->atoms.atom, com, FALSE);
 141         }
 142
 143         for (i = 0; i < ngx/3; i++)
 144         {
 145             /* put all waters in box */
 146             for (j = 0; j < DIM; j++)
 147             {
 148                 if (x0[index[3*i]][j] < 0)
 149                 {
 150                     x0[index[3*i]][j]   += box[j][j];
 151                     x0[index[3*i+1]][j] += box[j][j];
 152                     x0[index[3*i+2]][j] += box[j][j];
 153                 }
 154                 if (x0[index[3*i]][j] > box[j][j])
 155                 {
 156                     x0[index[3*i]][j]   -= box[j][j];
 157                     x0[index[3*i+1]][j] -= box[j][j];
 158                     x0[index[3*i+2]][j] -= box[j][j];
 159                 }
 160             }
 161
 162             for (j = 0; j < DIM; j++)
 163             {
 164                 dipole[j] =
 165                     x0[index[3*i]][j] * top->atoms.atom[index[3*i]].q +
 166                     x0[index[3*i+1]][j] * top->atoms.atom[index[3*i+1]].q +
 167                     x0[index[3*i+2]][j] * top->atoms.atom[index[3*i+2]].q;
 168             }
 169
 170             /* now we have a dipole vector. Might as well safe it. Then the
 171                rest depends on whether we're dealing with
 172                a flat or a spherical interface.
 173              */
 174
 175             if (bMicel)
 176             {                                          /* this is for spherical interfaces */
 177                 rvec_sub(com, x0[index[3*i]], normal); /* vector from Oxygen to COM */
 178                 slice = norm(normal)/(*slWidth);       /* spherical slice           */
 179
 180                 sum[slice]   += iprod(dipole, normal) / (norm(dipole) * norm(normal));
 181                 frame[slice] += iprod(dipole, normal) / (norm(dipole) * norm(normal));
 182                 count[slice]++;
 183
 184             }
 185             else
 186             {
 187                 /* this is for flat interfaces      */
 188
 189                 /* determine which slice atom is in */
 190                 slice = (x0[index[3*i]][axis] / (*slWidth));
 191                 if (slice < 0 || slice >= *nslices)
 192                 {
 193                     fprintf(stderr, "Coordinate: %f ", x0[index[3*i]][axis]);
 194                     fprintf(stderr, "HELP PANIC! slice = %d, OUT OF RANGE!\n", slice);
 195                 }
 196                 else
 197                 {
 198                     rvec_add(dipole, dip[slice], dip[slice]);
 199                     /* Add dipole to total. mag[slice] is total dipole in axis direction */
 200                     sum[slice]   += iprod(dipole, normal)/norm(dipole);
 201                     frame[slice] += iprod(dipole, normal)/norm(dipole);
 202                     /* increase count for that slice */
 203                     count[slice]++;
 204                 }
 205             }
 206         }
 207
 208     }
 209     while (read_next_x(oenv, status, &t, natoms, x0, box));
 210     /*********** done with status file **********/
 211
 212     fprintf(stderr, "\nRead trajectory. Printing parameters to file\n");
 213     gmx_rmpbc_done(gpbc);
 214
 215     for (i = 0; i < *nslices; i++) /* average over frames */
 216     {
 217         fprintf(stderr, "%d waters in slice %d\n", count[i], i);
 218         if (count[i] > 0) /* divide by number of molecules in each slice */
 219         {
 220             sum[i]     = sum[i] / count[i];
 221             dip[i][XX] = dip[i][XX] / count[i];
 222             dip[i][YY] = dip[i][YY] / count[i];
 223             dip[i][ZZ] = dip[i][ZZ] / count[i];
 224         }
 225         else
 226         {
 227             fprintf(stderr, "No water in slice %d\n", i);
 228         }
 229     }
 230
 231     *slOrder  = sum; /* copy a pointer, I hope */
 232     *slDipole = dip;
 233     sfree(x0);       /* free memory used by coordinate arrays */
 234 }
 235
 236 void h2order_plot(rvec dipole[], real order[], const char *afile,
 237                   int nslices, real slWidth, const output_env_t oenv)
 238 {
 239     FILE       *ord;              /* xvgr files with order parameters  */
 240     int         slice;            /* loop index     */
 241     char        buf[256];         /* for xvgr title */
 242     real        factor;           /* conversion to Debye from electron*nm */
 243
 244     /*  factor = 1e-9*1.60217733e-19/3.336e-30 */
 245     factor = 1.60217733/3.336e-2;
 246     fprintf(stderr, "%d slices\n", nslices);
 247     sprintf(buf, "Water orientation with respect to normal");
 248     ord = xvgropen(afile, buf,
 249                    "box (nm)", "mu_x, mu_y, mu_z (D), cosine with normal", oenv);
 250
 251     for (slice = 0; slice < nslices; slice++)
 252     {
 253         fprintf(ord, "%8.3f %8.3f %8.3f %8.3f %e\n", slWidth*slice,
 254                 factor*dipole[slice][XX], factor*dipole[slice][YY],
 255                 factor*dipole[slice][ZZ], order[slice]);
 256     }
 257
 258     ffclose(ord);
 259 }
 260
 261 int gmx_h2order(int argc, char *argv[])
 262 {
 263     const char        *desc[] = {
 264         "[TT]g_h2order[tt] computes the orientation of water molecules with respect to the normal",
 265         "of the box. The program determines the average cosine of the angle",
 266         "between the dipole moment of water and an axis of the box. The box is",
 267         "divided in slices and the average orientation per slice is printed.",
 268         "Each water molecule is assigned to a slice, per time frame, based on the",
 269         "position of the oxygen. When [TT]-nm[tt] is used, the angle between the water",
 270         "dipole and the axis from the center of mass to the oxygen is calculated",
 271         "instead of the angle between the dipole and a box axis."
 272     };
 273     static int         axis    = 2;           /* normal to memb. default z  */
 274     static const char *axtitle = "Z";
 275     static int         nslices = 0;           /* nr of slices defined       */
 276     t_pargs            pa[]    = {
 277         { "-d",   FALSE, etSTR, {&axtitle},
 278           "Take the normal on the membrane in direction X, Y or Z." },
 279         { "-sl",  FALSE, etINT, {&nslices},
 280           "Calculate order parameter as function of boxlength, dividing the box"
 281           " in this number of slices."}
 282     };
 283     const char        *bugs[] = {
 284         "The program assigns whole water molecules to a slice, based on the first "
 285         "atom of three in the index file group. It assumes an order O,H,H. "
 286         "Name is not important, but the order is. If this demand is not met, "
 287         "assigning molecules to slices is different."
 288     };
 289
 290     output_env_t       oenv;
 291     real              *slOrder,             /* av. cosine, per slice      */
 292                        slWidth = 0.0;       /* width of a slice           */
 293     rvec              *slDipole;
 294     char              *grpname,             /* groupnames                 */
 295     *micname;
 296     int                ngx,                 /* nr. of atomsin sol group   */
 297                        nmic = 0;            /* nr. of atoms in micelle    */
 298     t_topology        *top;                 /* topology           */
 299     int                ePBC;
 300     atom_id           *index,               /* indices for solvent group  */
 301     *micelle                  = NULL;
 302     gmx_bool           bMicel =  FALSE;     /* think we're a micel        */
 303     t_filenm           fnm[]  = {           /* files for g_order      */
 304         { efTRX, "-f", NULL,  ffREAD },     /* trajectory file            */
 305         { efNDX, NULL, NULL,  ffREAD },     /* index file         */
 306         { efNDX, "-nm", NULL, ffOPTRD },    /* index with micelle atoms   */
 307         { efTPX, NULL, NULL,  ffREAD },     /* topology file              */
 308         { efXVG, "-o",  "order", ffWRITE }, /* xvgr output file       */
 309     };
 310
 311 #define NFILE asize(fnm)
 312
 313     parse_common_args(&argc, argv,
 314                       PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
 315                       fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv);
 316     bMicel = opt2bSet("-nm", NFILE, fnm);
 317
 318     top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
 319
 320     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);
 321
 322     if (bMicel)
 323     {
 324         rd_index(opt2fn("-nm", NFILE, fnm), 1, &nmic, &micelle, &micname);
 325     }
 326
 327     calc_h2order(ftp2fn(efTRX, NFILE, fnm), index, ngx, &slDipole, &slOrder,
 328                  &slWidth, &nslices, top, ePBC, axis, bMicel, micelle, nmic,
 329                  oenv);
 330
 331     h2order_plot(slDipole, slOrder, opt2fn("-o", NFILE, fnm), nslices,
 332                  slWidth, oenv);
 333
 334     do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy"); /* view xvgr file */
 335     thanx(stderr);
 336
 337     return 0;
 338 }