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44 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/math/vec.h"
50 #include "gromacs/utility/futil.h"
56 #include "gromacs/fileio/tpxio.h"
57 #include "gromacs/fileio/trxio.h"
59 #include "gromacs/fileio/matio.h"
64 #include "gromacs/utility/fatalerror.h"
66 int gmx_densmap(int argc, char *argv[])
68 const char *desc[] = {
69 "[THISMODULE] computes 2D number-density maps.",
70 "It can make planar and axial-radial density maps.",
71 "The output [TT].xpm[tt] file can be visualized with for instance xv",
72 "and can be converted to postscript with [TT]xpm2ps[tt].",
73 "Optionally, output can be in text form to a [TT].dat[tt] file with [TT]-od[tt], instead of the usual [TT].xpm[tt] file with [TT]-o[tt].",
75 "The default analysis is a 2-D number-density map for a selected",
76 "group of atoms in the x-y plane.",
77 "The averaging direction can be changed with the option [TT]-aver[tt].",
78 "When [TT]-xmin[tt] and/or [TT]-xmax[tt] are set only atoms that are",
79 "within the limit(s) in the averaging direction are taken into account.",
80 "The grid spacing is set with the option [TT]-bin[tt].",
81 "When [TT]-n1[tt] or [TT]-n2[tt] is non-zero, the grid",
82 "size is set by this option.",
83 "Box size fluctuations are properly taken into account.",
85 "When options [TT]-amax[tt] and [TT]-rmax[tt] are set, an axial-radial",
86 "number-density map is made. Three groups should be supplied, the centers",
87 "of mass of the first two groups define the axis, the third defines the",
88 "analysis group. The axial direction goes from -amax to +amax, where",
89 "the center is defined as the midpoint between the centers of mass and",
90 "the positive direction goes from the first to the second center of mass.",
91 "The radial direction goes from 0 to rmax or from -rmax to +rmax",
92 "when the [TT]-mirror[tt] option has been set.",
94 "The normalization of the output is set with the [TT]-unit[tt] option.",
95 "The default produces a true number density. Unit [TT]nm-2[tt] leaves out",
96 "the normalization for the averaging or the angular direction.",
97 "Option [TT]count[tt] produces the count for each grid cell.",
98 "When you do not want the scale in the output to go",
99 "from zero to the maximum density, you can set the maximum",
100 "with the option [TT]-dmax[tt]."
102 static int n1 = 0, n2 = 0;
103 static real xmin = -1, xmax = -1, bin = 0.02, dmin = 0, dmax = 0, amax = 0, rmax = 0;
104 static gmx_bool bMirror = FALSE, bSums = FALSE;
105 static const char *eaver[] = { NULL, "z", "y", "x", NULL };
106 static const char *eunit[] = { NULL, "nm-3", "nm-2", "count", NULL };
109 { "-bin", FALSE, etREAL, {&bin},
111 { "-aver", FALSE, etENUM, {eaver},
112 "The direction to average over" },
113 { "-xmin", FALSE, etREAL, {&xmin},
114 "Minimum coordinate for averaging" },
115 { "-xmax", FALSE, etREAL, {&xmax},
116 "Maximum coordinate for averaging" },
117 { "-n1", FALSE, etINT, {&n1},
118 "Number of grid cells in the first direction" },
119 { "-n2", FALSE, etINT, {&n2},
120 "Number of grid cells in the second direction" },
121 { "-amax", FALSE, etREAL, {&amax},
122 "Maximum axial distance from the center"},
123 { "-rmax", FALSE, etREAL, {&rmax},
124 "Maximum radial distance" },
125 { "-mirror", FALSE, etBOOL, {&bMirror},
126 "Add the mirror image below the axial axis" },
127 { "-sums", FALSE, etBOOL, {&bSums},
128 "Print density sums (1D map) to stdout" },
129 { "-unit", FALSE, etENUM, {eunit},
130 "Unit for the output" },
131 { "-dmin", FALSE, etREAL, {&dmin},
132 "Minimum density in output"},
133 { "-dmax", FALSE, etREAL, {&dmax},
134 "Maximum density in output (0 means calculate it)"},
136 gmx_bool bXmin, bXmax, bRadial;
141 rvec *x, xcom[2], direction, center, dx;
145 int cav = 0, c1 = 0, c2 = 0, natoms;
146 char **grpname, title[256], buf[STRLEN];
148 int i, j, k, l, ngrps, anagrp, *gnx = NULL, nindex, nradial = 0, nfr, nmpower;
149 atom_id **ind = NULL, *index;
150 real **grid, maxgrid, m1, m2, box1, box2, *tickx, *tickz, invcellvol;
151 real invspa = 0, invspz = 0, axial, r, vol_old, vol, rowsum;
153 t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
155 const char *label[] = { "x (nm)", "y (nm)", "z (nm)" };
157 { efTRX, "-f", NULL, ffREAD },
158 { efTPS, NULL, NULL, ffOPTRD },
159 { efNDX, NULL, NULL, ffOPTRD },
160 { efDAT, "-od", "densmap", ffOPTWR },
161 { efXPM, "-o", "densmap", ffWRITE }
163 #define NFILE asize(fnm)
168 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
169 NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
174 bXmin = opt2parg_bSet("-xmin", npargs, pa);
175 bXmax = opt2parg_bSet("-xmax", npargs, pa);
176 bRadial = (amax > 0 || rmax > 0);
179 if (amax <= 0 || rmax <= 0)
181 gmx_fatal(FARGS, "Both amax and rmax should be larger than zero");
185 if (strcmp(eunit[0], "nm-3") == 0)
190 else if (strcmp(eunit[0], "nm-2") == 0)
201 if (ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm))
203 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box,
209 fprintf(stderr, "\nSelect an analysis group\n");
215 "\nSelect two groups to define the axis and an analysis group\n");
218 snew(grpname, ngrps);
220 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), ngrps, gnx, ind, grpname);
222 nindex = gnx[anagrp];
226 if ((gnx[0] > 1 || gnx[1] > 1) && !ftp2bSet(efTPS, NFILE, fnm))
228 gmx_fatal(FARGS, "No run input file was supplied (option -s), this is required for the center of mass calculation");
234 case 'x': cav = XX; c1 = YY; c2 = ZZ; break;
235 case 'y': cav = YY; c1 = XX; c2 = ZZ; break;
236 case 'z': cav = ZZ; c1 = XX; c2 = YY; break;
239 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
245 n1 = (int)(box[c1][c1]/bin + 0.5);
249 n2 = (int)(box[c2][c2]/bin + 0.5);
254 n1 = (int)(2*amax/bin + 0.5);
255 nradial = (int)(rmax/bin + 0.5);
256 invspa = n1/(2*amax);
257 invspz = nradial/rmax;
269 for (i = 0; i < n1; i++)
286 invcellvol /= det(box);
288 else if (nmpower == -2)
290 invcellvol /= box[c1][c1]*box[c2][c2];
292 for (i = 0; i < nindex; i++)
295 if ((!bXmin || x[j][cav] >= xmin) &&
296 (!bXmax || x[j][cav] <= xmax))
298 m1 = x[j][c1]/box[c1][c1];
307 m2 = x[j][c2]/box[c2][c2];
316 grid[(int)(m1*n1)][(int)(m2*n2)] += invcellvol;
322 set_pbc(&pbc, ePBC, box);
323 for (i = 0; i < 2; i++)
327 /* One atom, just copy the coordinates */
328 copy_rvec(x[ind[i][0]], xcom[i]);
332 /* Calculate the center of mass */
335 for (j = 0; j < gnx[i]; j++)
338 m = top.atoms.atom[k].m;
339 for (l = 0; l < DIM; l++)
341 xcom[i][l] += m*x[k][l];
345 svmul(1/mtot, xcom[i], xcom[i]);
348 pbc_dx(&pbc, xcom[1], xcom[0], direction);
349 for (i = 0; i < DIM; i++)
351 center[i] = xcom[0][i] + 0.5*direction[i];
353 unitv(direction, direction);
354 for (i = 0; i < nindex; i++)
357 pbc_dx(&pbc, x[j], center, dx);
358 axial = iprod(dx, direction);
359 r = sqrt(norm2(dx) - axial*axial);
360 if (axial >= -amax && axial < amax && r < rmax)
366 grid[(int)((axial + amax)*invspa)][(int)(r*invspz)] += 1;
372 while (read_next_x(oenv, status, &t, x, box));
375 /* normalize gridpoints */
379 for (i = 0; i < n1; i++)
381 for (j = 0; j < n2; j++)
384 if (grid[i][j] > maxgrid)
386 maxgrid = grid[i][j];
393 for (i = 0; i < n1; i++)
396 for (j = 0; j < nradial; j++)
400 case -3: vol = M_PI*(j+1)*(j+1)/(invspz*invspz*invspa); break;
401 case -2: vol = (j+1)/(invspz*invspa); break;
402 default: vol = j+1; break;
412 grid[i][k] /= nfr*(vol - vol_old);
415 grid[i][nradial-1-j] = grid[i][k];
418 if (grid[i][k] > maxgrid)
420 maxgrid = grid[i][k];
425 fprintf(stdout, "\n The maximum density is %f %s\n", maxgrid, unit);
435 /* normalize box-axes */
438 for (i = 0; i <= n1; i++)
440 tickx[i] = i*box1/n1;
442 for (i = 0; i <= n2; i++)
444 tickz[i] = i*box2/n2;
449 for (i = 0; i <= n1; i++)
451 tickx[i] = i/invspa - amax;
455 for (i = 0; i <= n2; i++)
457 tickz[i] = i/invspz - rmax;
462 for (i = 0; i <= n2; i++)
471 for (i = 0; i < n1; ++i)
473 fprintf(stdout, "Density sums:\n");
475 for (j = 0; j < n2; ++j)
477 rowsum += grid[i][j];
479 fprintf(stdout, "%g\t", rowsum);
481 fprintf(stdout, "\n");
484 sprintf(buf, "%s number density", grpname[anagrp]);
485 if (!bRadial && (bXmin || bXmax))
489 sprintf(buf+strlen(buf), ", %c > %g nm", eaver[0][0], xmin);
493 sprintf(buf+strlen(buf), ", %c < %g nm", eaver[0][0], xmax);
497 sprintf(buf+strlen(buf), ", %c: %g - %g nm", eaver[0][0], xmin, xmax);
500 if (ftp2bSet(efDAT, NFILE, fnm))
502 fp = gmx_ffopen(ftp2fn(efDAT, NFILE, fnm), "w");
503 /*optional text form output: first row is tickz; first col is tickx */
505 for (j = 0; j < n2; ++j)
507 fprintf(fp, "%g\t", tickz[j]);
511 for (i = 0; i < n1; ++i)
513 fprintf(fp, "%g\t", tickx[i]);
514 for (j = 0; j < n2; ++j)
516 fprintf(fp, "%g\t", grid[i][j]);
524 fp = gmx_ffopen(ftp2fn(efXPM, NFILE, fnm), "w");
525 write_xpm(fp, MAT_SPATIAL_X | MAT_SPATIAL_Y, buf, unit,
526 bRadial ? "axial (nm)" : label[c1], bRadial ? "r (nm)" : label[c2],
527 n1, n2, tickx, tickz, grid, dmin, maxgrid, rlo, rhi, &nlev);
531 do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);