src/gromacs/gmxana/gmx_h2order.c

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  37 #include "gmxpre.h"
  38
  39 #include "config.h"
  40
  41 #include <math.h>
  42 #include <string.h>
  43
  44 #include "gromacs/legacyheaders/typedefs.h"
  45 #include "gromacs/utility/smalloc.h"
  46 #include "gromacs/legacyheaders/macros.h"
  47 #include "princ.h"
  48 #include "gromacs/pbcutil/rmpbc.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/fileio/xvgr.h"
  51 #include "gromacs/legacyheaders/viewit.h"
  52 #include "gromacs/utility/futil.h"
  53 #include "gromacs/commandline/pargs.h"
  54 #include "gromacs/topology/index.h"
  55 #include "gmx_ana.h"
  56 #include "gromacs/fileio/trxio.h"
  57
  58 #include "gromacs/utility/fatalerror.h"
  59
  60 /****************************************************************************/
  61 /* This program calculates the ordering of water molecules across a box, as */
  62 /* function of the z-coordinate. This implies averaging over slices and over*/
  63 /* time. Output is the average cos of the angle of the dipole with the      */
  64 /* normal, per slice.                                                       */
  65 /* In addition, it calculates the average dipole moment itself in three     */
  66 /* directions.                                                              */
  67 /****************************************************************************/
  68
  69 void calc_h2order(const char *fn, atom_id index[], int ngx, rvec **slDipole,
  70                   real **slOrder, real *slWidth, int *nslices,
  71                   t_topology *top, int ePBC,
  72                   int axis, gmx_bool bMicel, atom_id micel[], int nmic,
  73                   const output_env_t oenv)
  74 {
  75     rvec *x0,            /* coordinates with pbc */
  76           dipole,        /* dipole moment due to one molecules */
  77           normal,
  78           com;           /* center of mass of micel, with bMicel */
  79     rvec        *dip;    /* sum of dipoles, unnormalized */
  80     matrix       box;    /* box (3x3) */
  81     t_trxstatus *status;
  82     real         t,      /* time from trajectory */
  83     *sum,                /* sum of all cosines of dipoles, per slice */
  84     *frame;              /* order over one frame */
  85     int natoms,          /* nr. atoms in trj */
  86         i, j, teller = 0,
  87         slice = 0,       /* current slice number */
  88     *count;              /* nr. of atoms in one slice */
  89     gmx_rmpbc_t  gpbc = NULL;
  90
  91     if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
  92     {
  93         gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
  94     }
  95
  96     if (!*nslices)
  97     {
  98         *nslices = (int)(box[axis][axis] * 10); /* default value */
  99
 100
 101     }
 102     switch (axis)
 103     {
 104         case 0:
 105             normal[0] = 1; normal[1] = 0; normal[2] = 0;
 106             break;
 107         case 1:
 108             normal[0] = 0; normal[1] = 1; normal[2] = 0;
 109             break;
 110         case 2:
 111             normal[0] = 0; normal[1] = 0; normal[2] = 1;
 112             break;
 113         default:
 114             gmx_fatal(FARGS, "No valid value for -axis-. Exiting.\n");
 115             /* make compiler happy */
 116             normal[0] = 1; normal[1] = 0; normal[2] = 0;
 117     }
 118
 119     clear_rvec(dipole);
 120     snew(count, *nslices);
 121     snew(sum, *nslices);
 122     snew(dip, *nslices);
 123     snew(frame, *nslices);
 124
 125     *slWidth = box[axis][axis]/(*nslices);
 126     fprintf(stderr, "Box divided in %d slices. Initial width of slice: %f\n",
 127             *nslices, *slWidth);
 128
 129     teller = 0;
 130
 131     gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
 132     /*********** Start processing trajectory ***********/
 133     do
 134     {
 135         *slWidth = box[axis][axis]/(*nslices);
 136         teller++;
 137
 138         gmx_rmpbc(gpbc, natoms, box, x0);
 139
 140         if (bMicel)
 141         {
 142             calc_xcm(x0, nmic, micel, top->atoms.atom, com, FALSE);
 143         }
 144
 145         for (i = 0; i < ngx/3; i++)
 146         {
 147             /* put all waters in box */
 148             for (j = 0; j < DIM; j++)
 149             {
 150                 if (x0[index[3*i]][j] < 0)
 151                 {
 152                     x0[index[3*i]][j]   += box[j][j];
 153                     x0[index[3*i+1]][j] += box[j][j];
 154                     x0[index[3*i+2]][j] += box[j][j];
 155                 }
 156                 if (x0[index[3*i]][j] > box[j][j])
 157                 {
 158                     x0[index[3*i]][j]   -= box[j][j];
 159                     x0[index[3*i+1]][j] -= box[j][j];
 160                     x0[index[3*i+2]][j] -= box[j][j];
 161                 }
 162             }
 163
 164             for (j = 0; j < DIM; j++)
 165             {
 166                 dipole[j] =
 167                     x0[index[3*i]][j] * top->atoms.atom[index[3*i]].q +
 168                     x0[index[3*i+1]][j] * top->atoms.atom[index[3*i+1]].q +
 169                     x0[index[3*i+2]][j] * top->atoms.atom[index[3*i+2]].q;
 170             }
 171
 172             /* now we have a dipole vector. Might as well safe it. Then the
 173                rest depends on whether we're dealing with
 174                a flat or a spherical interface.
 175              */
 176
 177             if (bMicel)
 178             {                                          /* this is for spherical interfaces */
 179                 rvec_sub(com, x0[index[3*i]], normal); /* vector from Oxygen to COM */
 180                 slice = norm(normal)/(*slWidth);       /* spherical slice           */
 181
 182                 sum[slice]   += iprod(dipole, normal) / (norm(dipole) * norm(normal));
 183                 frame[slice] += iprod(dipole, normal) / (norm(dipole) * norm(normal));
 184                 count[slice]++;
 185
 186             }
 187             else
 188             {
 189                 /* this is for flat interfaces      */
 190
 191                 /* determine which slice atom is in */
 192                 slice = (x0[index[3*i]][axis] / (*slWidth));
 193                 if (slice < 0 || slice >= *nslices)
 194                 {
 195                     fprintf(stderr, "Coordinate: %f ", x0[index[3*i]][axis]);
 196                     fprintf(stderr, "HELP PANIC! slice = %d, OUT OF RANGE!\n", slice);
 197                 }
 198                 else
 199                 {
 200                     rvec_add(dipole, dip[slice], dip[slice]);
 201                     /* Add dipole to total. mag[slice] is total dipole in axis direction */
 202                     sum[slice]   += iprod(dipole, normal)/norm(dipole);
 203                     frame[slice] += iprod(dipole, normal)/norm(dipole);
 204                     /* increase count for that slice */
 205                     count[slice]++;
 206                 }
 207             }
 208         }
 209
 210     }
 211     while (read_next_x(oenv, status, &t, x0, box));
 212     /*********** done with status file **********/
 213
 214     fprintf(stderr, "\nRead trajectory. Printing parameters to file\n");
 215     gmx_rmpbc_done(gpbc);
 216
 217     for (i = 0; i < *nslices; i++) /* average over frames */
 218     {
 219         fprintf(stderr, "%d waters in slice %d\n", count[i], i);
 220         if (count[i] > 0) /* divide by number of molecules in each slice */
 221         {
 222             sum[i]     = sum[i] / count[i];
 223             dip[i][XX] = dip[i][XX] / count[i];
 224             dip[i][YY] = dip[i][YY] / count[i];
 225             dip[i][ZZ] = dip[i][ZZ] / count[i];
 226         }
 227         else
 228         {
 229             fprintf(stderr, "No water in slice %d\n", i);
 230         }
 231     }
 232
 233     *slOrder  = sum; /* copy a pointer, I hope */
 234     *slDipole = dip;
 235     sfree(x0);       /* free memory used by coordinate arrays */
 236 }
 237
 238 void h2order_plot(rvec dipole[], real order[], const char *afile,
 239                   int nslices, real slWidth, const output_env_t oenv)
 240 {
 241     FILE       *ord;              /* xvgr files with order parameters  */
 242     int         slice;            /* loop index     */
 243     char        buf[256];         /* for xvgr title */
 244     real        factor;           /* conversion to Debye from electron*nm */
 245
 246     /*  factor = 1e-9*1.60217733e-19/3.336e-30 */
 247     factor = 1.60217733/3.336e-2;
 248     fprintf(stderr, "%d slices\n", nslices);
 249     sprintf(buf, "Water orientation with respect to normal");
 250     ord = xvgropen(afile, buf,
 251                    "box (nm)", "mu_x, mu_y, mu_z (D), cosine with normal", oenv);
 252
 253     for (slice = 0; slice < nslices; slice++)
 254     {
 255         fprintf(ord, "%8.3f %8.3f %8.3f %8.3f %e\n", slWidth*slice,
 256                 factor*dipole[slice][XX], factor*dipole[slice][YY],
 257                 factor*dipole[slice][ZZ], order[slice]);
 258     }
 259
 260     gmx_ffclose(ord);
 261 }
 262
 263 int gmx_h2order(int argc, char *argv[])
 264 {
 265     const char        *desc[] = {
 266         "[THISMODULE] computes the orientation of water molecules with respect to the normal",
 267         "of the box. The program determines the average cosine of the angle",
 268         "between the dipole moment of water and an axis of the box. The box is",
 269         "divided in slices and the average orientation per slice is printed.",
 270         "Each water molecule is assigned to a slice, per time frame, based on the",
 271         "position of the oxygen. When [TT]-nm[tt] is used, the angle between the water",
 272         "dipole and the axis from the center of mass to the oxygen is calculated",
 273         "instead of the angle between the dipole and a box axis."
 274     };
 275     static int         axis    = 2;           /* normal to memb. default z  */
 276     static const char *axtitle = "Z";
 277     static int         nslices = 0;           /* nr of slices defined       */
 278     t_pargs            pa[]    = {
 279         { "-d",   FALSE, etSTR, {&axtitle},
 280           "Take the normal on the membrane in direction X, Y or Z." },
 281         { "-sl",  FALSE, etINT, {&nslices},
 282           "Calculate order parameter as function of boxlength, dividing the box"
 283           " in this number of slices."}
 284     };
 285     const char        *bugs[] = {
 286         "The program assigns whole water molecules to a slice, based on the first "
 287         "atom of three in the index file group. It assumes an order O,H,H. "
 288         "Name is not important, but the order is. If this demand is not met, "
 289         "assigning molecules to slices is different."
 290     };
 291
 292     output_env_t       oenv;
 293     real              *slOrder,             /* av. cosine, per slice      */
 294                        slWidth = 0.0;       /* width of a slice           */
 295     rvec              *slDipole;
 296     char              *grpname,             /* groupnames                 */
 297     *micname;
 298     int                ngx,                 /* nr. of atomsin sol group   */
 299                        nmic = 0;            /* nr. of atoms in micelle    */
 300     t_topology        *top;                 /* topology           */
 301     int                ePBC;
 302     atom_id           *index,               /* indices for solvent group  */
 303     *micelle                  = NULL;
 304     gmx_bool           bMicel =  FALSE;     /* think we're a micel        */
 305     t_filenm           fnm[]  = {           /* files for g_order      */
 306         { efTRX, "-f", NULL,  ffREAD },     /* trajectory file            */
 307         { efNDX, NULL, NULL,  ffREAD },     /* index file         */
 308         { efNDX, "-nm", NULL, ffOPTRD },    /* index with micelle atoms   */
 309         { efTPX, NULL, NULL,  ffREAD },     /* topology file              */
 310         { efXVG, "-o",  "order", ffWRITE }, /* xvgr output file       */
 311     };
 312
 313 #define NFILE asize(fnm)
 314
 315     if (!parse_common_args(&argc, argv,
 316                            PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
 317                            fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
 318     {
 319         return 0;
 320     }
 321     bMicel = opt2bSet("-nm", NFILE, fnm);
 322
 323     top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
 324
 325     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);
 326
 327     if (bMicel)
 328     {
 329         rd_index(opt2fn("-nm", NFILE, fnm), 1, &nmic, &micelle, &micname);
 330     }
 331
 332     calc_h2order(ftp2fn(efTRX, NFILE, fnm), index, ngx, &slDipole, &slOrder,
 333                  &slWidth, &nslices, top, ePBC, axis, bMicel, micelle, nmic,
 334                  oenv);
 335
 336     h2order_plot(slDipole, slOrder, opt2fn("-o", NFILE, fnm), nslices,
 337                  slWidth, oenv);
 338
 339     do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy"); /* view xvgr file */
 340
 341     return 0;
 342 }