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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/fileio/matio.h"
44 #include "gromacs/fileio/tpxio.h"
45 #include "gromacs/fileio/trxio.h"
46 #include "gromacs/gmxana/gmx_ana.h"
47 #include "gromacs/gmxana/gstat.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/txtdump.h"
50 #include "gromacs/legacyheaders/typedefs.h"
51 #include "gromacs/legacyheaders/viewit.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/pbcutil/pbc.h"
54 #include "gromacs/topology/index.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/futil.h"
57 #include "gromacs/utility/smalloc.h"
59 int gmx_densmap(int argc, char *argv[])
61 const char *desc[] = {
62 "[THISMODULE] computes 2D number-density maps.",
63 "It can make planar and axial-radial density maps.",
64 "The output [REF].xpm[ref] file can be visualized with for instance xv",
65 "and can be converted to postscript with [TT]xpm2ps[tt].",
66 "Optionally, output can be in text form to a [REF].dat[ref] file with [TT]-od[tt], instead of the usual [REF].xpm[ref] file with [TT]-o[tt].",
68 "The default analysis is a 2-D number-density map for a selected",
69 "group of atoms in the x-y plane.",
70 "The averaging direction can be changed with the option [TT]-aver[tt].",
71 "When [TT]-xmin[tt] and/or [TT]-xmax[tt] are set only atoms that are",
72 "within the limit(s) in the averaging direction are taken into account.",
73 "The grid spacing is set with the option [TT]-bin[tt].",
74 "When [TT]-n1[tt] or [TT]-n2[tt] is non-zero, the grid",
75 "size is set by this option.",
76 "Box size fluctuations are properly taken into account.",
78 "When options [TT]-amax[tt] and [TT]-rmax[tt] are set, an axial-radial",
79 "number-density map is made. Three groups should be supplied, the centers",
80 "of mass of the first two groups define the axis, the third defines the",
81 "analysis group. The axial direction goes from -amax to +amax, where",
82 "the center is defined as the midpoint between the centers of mass and",
83 "the positive direction goes from the first to the second center of mass.",
84 "The radial direction goes from 0 to rmax or from -rmax to +rmax",
85 "when the [TT]-mirror[tt] option has been set.",
87 "The normalization of the output is set with the [TT]-unit[tt] option.",
88 "The default produces a true number density. Unit [TT]nm-2[tt] leaves out",
89 "the normalization for the averaging or the angular direction.",
90 "Option [TT]count[tt] produces the count for each grid cell.",
91 "When you do not want the scale in the output to go",
92 "from zero to the maximum density, you can set the maximum",
93 "with the option [TT]-dmax[tt]."
95 static int n1 = 0, n2 = 0;
96 static real xmin = -1, xmax = -1, bin = 0.02, dmin = 0, dmax = 0, amax = 0, rmax = 0;
97 static gmx_bool bMirror = FALSE, bSums = FALSE;
98 static const char *eaver[] = { NULL, "z", "y", "x", NULL };
99 static const char *eunit[] = { NULL, "nm-3", "nm-2", "count", NULL };
102 { "-bin", FALSE, etREAL, {&bin},
104 { "-aver", FALSE, etENUM, {eaver},
105 "The direction to average over" },
106 { "-xmin", FALSE, etREAL, {&xmin},
107 "Minimum coordinate for averaging" },
108 { "-xmax", FALSE, etREAL, {&xmax},
109 "Maximum coordinate for averaging" },
110 { "-n1", FALSE, etINT, {&n1},
111 "Number of grid cells in the first direction" },
112 { "-n2", FALSE, etINT, {&n2},
113 "Number of grid cells in the second direction" },
114 { "-amax", FALSE, etREAL, {&amax},
115 "Maximum axial distance from the center"},
116 { "-rmax", FALSE, etREAL, {&rmax},
117 "Maximum radial distance" },
118 { "-mirror", FALSE, etBOOL, {&bMirror},
119 "Add the mirror image below the axial axis" },
120 { "-sums", FALSE, etBOOL, {&bSums},
121 "Print density sums (1D map) to stdout" },
122 { "-unit", FALSE, etENUM, {eunit},
123 "Unit for the output" },
124 { "-dmin", FALSE, etREAL, {&dmin},
125 "Minimum density in output"},
126 { "-dmax", FALSE, etREAL, {&dmax},
127 "Maximum density in output (0 means calculate it)"},
129 gmx_bool bXmin, bXmax, bRadial;
134 rvec *x, xcom[2], direction, center, dx;
138 int cav = 0, c1 = 0, c2 = 0, natoms;
139 char **grpname, title[256], buf[STRLEN];
141 int i, j, k, l, ngrps, anagrp, *gnx = NULL, nindex, nradial = 0, nfr, nmpower;
142 atom_id **ind = NULL, *index;
143 real **grid, maxgrid, m1, m2, box1, box2, *tickx, *tickz, invcellvol;
144 real invspa = 0, invspz = 0, axial, r, vol_old, vol, rowsum;
146 t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
148 const char *label[] = { "x (nm)", "y (nm)", "z (nm)" };
150 { efTRX, "-f", NULL, ffREAD },
151 { efTPS, NULL, NULL, ffOPTRD },
152 { efNDX, NULL, NULL, ffOPTRD },
153 { efDAT, "-od", "densmap", ffOPTWR },
154 { efXPM, "-o", "densmap", ffWRITE }
156 #define NFILE asize(fnm)
161 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
162 NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
167 bXmin = opt2parg_bSet("-xmin", npargs, pa);
168 bXmax = opt2parg_bSet("-xmax", npargs, pa);
169 bRadial = (amax > 0 || rmax > 0);
172 if (amax <= 0 || rmax <= 0)
174 gmx_fatal(FARGS, "Both amax and rmax should be larger than zero");
178 if (strcmp(eunit[0], "nm-3") == 0)
183 else if (strcmp(eunit[0], "nm-2") == 0)
194 if (ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm))
196 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box,
202 fprintf(stderr, "\nSelect an analysis group\n");
208 "\nSelect two groups to define the axis and an analysis group\n");
211 snew(grpname, ngrps);
213 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), ngrps, gnx, ind, grpname);
215 nindex = gnx[anagrp];
219 if ((gnx[0] > 1 || gnx[1] > 1) && !ftp2bSet(efTPS, NFILE, fnm))
221 gmx_fatal(FARGS, "No run input file was supplied (option -s), this is required for the center of mass calculation");
227 case 'x': cav = XX; c1 = YY; c2 = ZZ; break;
228 case 'y': cav = YY; c1 = XX; c2 = ZZ; break;
229 case 'z': cav = ZZ; c1 = XX; c2 = YY; break;
232 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
238 n1 = (int)(box[c1][c1]/bin + 0.5);
242 n2 = (int)(box[c2][c2]/bin + 0.5);
247 n1 = (int)(2*amax/bin + 0.5);
248 nradial = (int)(rmax/bin + 0.5);
249 /* cppcheck-suppress zerodiv fixed in 1.68-dev */
250 invspa = n1/(2*amax);
251 /* cppcheck-suppress zerodiv fixed in 1.68-dev */
252 invspz = nradial/rmax;
264 for (i = 0; i < n1; i++)
281 invcellvol /= det(box);
283 else if (nmpower == -2)
285 invcellvol /= box[c1][c1]*box[c2][c2];
287 for (i = 0; i < nindex; i++)
290 if ((!bXmin || x[j][cav] >= xmin) &&
291 (!bXmax || x[j][cav] <= xmax))
293 m1 = x[j][c1]/box[c1][c1];
302 m2 = x[j][c2]/box[c2][c2];
311 grid[(int)(m1*n1)][(int)(m2*n2)] += invcellvol;
317 set_pbc(&pbc, ePBC, box);
318 for (i = 0; i < 2; i++)
322 /* One atom, just copy the coordinates */
323 copy_rvec(x[ind[i][0]], xcom[i]);
327 /* Calculate the center of mass */
330 for (j = 0; j < gnx[i]; j++)
333 m = top.atoms.atom[k].m;
334 for (l = 0; l < DIM; l++)
336 xcom[i][l] += m*x[k][l];
340 svmul(1/mtot, xcom[i], xcom[i]);
343 pbc_dx(&pbc, xcom[1], xcom[0], direction);
344 for (i = 0; i < DIM; i++)
346 center[i] = xcom[0][i] + 0.5*direction[i];
348 unitv(direction, direction);
349 for (i = 0; i < nindex; i++)
352 pbc_dx(&pbc, x[j], center, dx);
353 axial = iprod(dx, direction);
354 r = sqrt(norm2(dx) - axial*axial);
355 if (axial >= -amax && axial < amax && r < rmax)
361 grid[(int)((axial + amax)*invspa)][(int)(r*invspz)] += 1;
367 while (read_next_x(oenv, status, &t, x, box));
370 /* normalize gridpoints */
374 for (i = 0; i < n1; i++)
376 for (j = 0; j < n2; j++)
379 if (grid[i][j] > maxgrid)
381 maxgrid = grid[i][j];
388 for (i = 0; i < n1; i++)
391 for (j = 0; j < nradial; j++)
395 case -3: vol = M_PI*(j+1)*(j+1)/(invspz*invspz*invspa); break;
396 case -2: vol = (j+1)/(invspz*invspa); break;
397 default: vol = j+1; break;
407 grid[i][k] /= nfr*(vol - vol_old);
410 grid[i][nradial-1-j] = grid[i][k];
413 if (grid[i][k] > maxgrid)
415 maxgrid = grid[i][k];
420 fprintf(stdout, "\n The maximum density is %f %s\n", maxgrid, unit);
430 /* normalize box-axes */
433 for (i = 0; i <= n1; i++)
435 tickx[i] = i*box1/n1;
437 for (i = 0; i <= n2; i++)
439 tickz[i] = i*box2/n2;
444 for (i = 0; i <= n1; i++)
446 tickx[i] = i/invspa - amax;
450 for (i = 0; i <= n2; i++)
452 tickz[i] = i/invspz - rmax;
457 for (i = 0; i <= n2; i++)
466 for (i = 0; i < n1; ++i)
468 fprintf(stdout, "Density sums:\n");
470 for (j = 0; j < n2; ++j)
472 rowsum += grid[i][j];
474 fprintf(stdout, "%g\t", rowsum);
476 fprintf(stdout, "\n");
479 sprintf(buf, "%s number density", grpname[anagrp]);
480 if (!bRadial && (bXmin || bXmax))
484 sprintf(buf+strlen(buf), ", %c > %g nm", eaver[0][0], xmin);
488 sprintf(buf+strlen(buf), ", %c < %g nm", eaver[0][0], xmax);
492 sprintf(buf+strlen(buf), ", %c: %g - %g nm", eaver[0][0], xmin, xmax);
495 if (ftp2bSet(efDAT, NFILE, fnm))
497 fp = gmx_ffopen(ftp2fn(efDAT, NFILE, fnm), "w");
498 /*optional text form output: first row is tickz; first col is tickx */
500 for (j = 0; j < n2; ++j)
502 fprintf(fp, "%g\t", tickz[j]);
506 for (i = 0; i < n1; ++i)
508 fprintf(fp, "%g\t", tickx[i]);
509 for (j = 0; j < n2; ++j)
511 fprintf(fp, "%g\t", grid[i][j]);
519 fp = gmx_ffopen(ftp2fn(efXPM, NFILE, fnm), "w");
520 write_xpm(fp, MAT_SPATIAL_X | MAT_SPATIAL_Y, buf, unit,
521 bRadial ? "axial (nm)" : label[c1], bRadial ? "r (nm)" : label[c2],
522 n1, n2, tickx, tickz, grid, dmin, maxgrid, rlo, rhi, &nlev);
526 do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);