3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
11 * Copyright (c) 1991-2001
12 * BIOSON Research Institute, Dept. of Biophysical Chemistry
13 * University of Groningen, The Netherlands
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
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25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
33 * Gyas ROwers Mature At Cryogenic Speed
46 #include "gromacs/fileio/tpxio.h"
47 #include "gromacs/fileio/trxio.h"
56 static const double bohr = 0.529177249; /* conversion factor to compensate for VMD plugin conversion... */
58 static void mequit(void)
60 printf("Memory allocation error\n");
64 int gmx_spatial(int argc, char *argv[])
66 const char *desc[] = {
67 "[TT]g_spatial[tt] calculates the spatial distribution function and ",
68 "outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
69 "This was developed from template.c (GROMACS-3.3). ",
70 "For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated ",
71 "in about 30 minutes, with most of the time dedicated to the two runs through ",
72 "[TT]trjconv[tt] that are required to center everything properly. ",
73 "This also takes a whole bunch of space (3 copies of the [TT].xtc[tt] file). ",
74 "Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
75 "3-4 atoms in a widely mobile group (like a free amino acid in solution) works ",
76 "well, or select the protein backbone in a stable folded structure to get the SDF ",
77 "of solvent and look at the time-averaged solvation shell. ",
78 "It is also possible using this program to generate the SDF based on some arbitrary ",
79 "Cartesian coordinate. To do that, simply omit the preliminary [TT]trjconv[tt] steps. \n",
81 "1. Use [TT]make_ndx[tt] to create a group containing the atoms around which you want the SDF \n",
82 "2. [TT]trjconv -s a.tpr -f a.xtc -o b.xtc -boxcenter tric -ur compact -pbc none[tt] \n",
83 "3. [TT]trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans[tt] \n",
84 "4. run [TT]g_spatial[tt] on the [TT].xtc[tt] output of step #3. \n",
85 "5. Load [TT]grid.cube[tt] into VMD and view as an isosurface. \n",
86 "[BB]Note[bb] that systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
88 "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
89 "However, the preparatory [TT]-fit rot+trans[tt] option to [TT]trjconv[tt] implies that your system will be rotating ",
90 "and translating in space (in order that the selected group does not). Therefore the values that are ",
91 "returned will only be valid for some region around your central group/coordinate that has full overlap ",
92 "with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
93 "It is up to the user to ensure that this is the case. \n",
95 "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
96 "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)",
97 "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
98 "with an increased [TT]-nab[tt] value. \n",
100 "To reduce the amount of space and time required, you can output only the coords ",
101 "that are going to be used in the first and subsequent run through [TT]trjconv[tt]. ",
102 "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
103 "memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt] ",
107 static gmx_bool bPBC = FALSE;
108 static gmx_bool bSHIFT = FALSE;
109 static int iIGNOREOUTER = -1; /*Positive values may help if the surface is spikey */
110 static gmx_bool bCUTDOWN = TRUE;
111 static real rBINWIDTH = 0.05; /* nm */
112 static gmx_bool bCALCDIV = TRUE;
116 { "-pbc", FALSE, etBOOL, {&bPBC},
117 "Use periodic boundary conditions for computing distances" },
118 { "-div", FALSE, etBOOL, {&bCALCDIV},
119 "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" },
120 { "-ign", FALSE, etINT, {&iIGNOREOUTER},
121 "Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible)" },
122 /* { "-cut", bCUTDOWN, etBOOL, {&bCUTDOWN},*/
123 /* "Display a total cube that is of minimal size" }, */
124 { "-bin", FALSE, etREAL, {&rBINWIDTH},
125 "Width of the bins (nm)" },
126 { "-nab", FALSE, etINT, {&iNAB},
127 "Number of additional bins to ensure proper memory allocation" }
136 rvec *xtop, *shx[26];
139 int flags = TRX_READ_X;
143 char *grpnm, *grpnmp;
144 atom_id *index, *indexp;
148 long ***bin = (long ***)NULL;
151 long x, y, z, minx, miny, minz, maxx, maxy, maxz;
156 gmx_rmpbc_t gpbc = NULL;
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 }
164 #define NFILE asize(fnm)
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, 0, NULL, &oenv))
174 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
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);
183 /* The first time we read data is a little special */
184 natoms = read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, flags);
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)
192 if (fr.x[i][XX] < MINBIN[XX])
194 MINBIN[XX] = fr.x[i][XX];
196 if (fr.x[i][XX] > MAXBIN[XX])
198 MAXBIN[XX] = fr.x[i][XX];
200 if (fr.x[i][YY] < MINBIN[YY])
202 MINBIN[YY] = fr.x[i][YY];
204 if (fr.x[i][YY] > MAXBIN[YY])
206 MAXBIN[YY] = fr.x[i][YY];
208 if (fr.x[i][ZZ] < MINBIN[ZZ])
210 MINBIN[ZZ] = fr.x[i][ZZ];
212 if (fr.x[i][ZZ] > MAXBIN[ZZ])
214 MAXBIN[ZZ] = fr.x[i][ZZ];
217 for (i = ZZ; i >= XX; --i)
219 MAXBIN[i] = (ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH)+(double)iNAB)*rBINWIDTH+MINBIN[i];
220 MINBIN[i] -= (double)iNAB*rBINWIDTH;
221 nbin[i] = (long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
223 bin = (long ***)malloc(nbin[XX]*sizeof(long **));
228 for (i = 0; i < nbin[XX]; ++i)
230 bin[i] = (long **)malloc(nbin[YY]*sizeof(long *));
235 for (j = 0; j < nbin[YY]; ++j)
237 bin[i][j] = (long *)calloc(nbin[ZZ], sizeof(long));
244 copy_mat(box, box_pbc);
246 minx = miny = minz = 999;
247 maxx = maxy = maxz = 0;
251 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
253 /* This is the main loop over frames */
256 /* Must init pbc every step because of pressure coupling */
258 copy_mat(box, box_pbc);
261 gmx_rmpbc_trxfr(gpbc, &fr);
262 set_pbc(&pbc, ePBC, box_pbc);
265 for (i = 0; i < nidx; i++)
267 if (fr.x[index[i]][XX] < MINBIN[XX] || fr.x[index[i]][XX] > MAXBIN[XX] ||
268 fr.x[index[i]][YY] < MINBIN[YY] || fr.x[index[i]][YY] > MAXBIN[YY] ||
269 fr.x[index[i]][ZZ] < MINBIN[ZZ] || fr.x[index[i]][ZZ] > MAXBIN[ZZ])
271 printf("There was an item outside of the allocated memory. Increase the value given with the -nab option.\n");
272 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]);
273 printf("Memory was required for [%f,%f,%f]\n", fr.x[index[i]][XX], fr.x[index[i]][YY], fr.x[index[i]][ZZ]);
276 x = (long)ceil((fr.x[index[i]][XX]-MINBIN[XX])/rBINWIDTH);
277 y = (long)ceil((fr.x[index[i]][YY]-MINBIN[YY])/rBINWIDTH);
278 z = (long)ceil((fr.x[index[i]][ZZ]-MINBIN[ZZ])/rBINWIDTH);
306 /* printf("%f\t%f\t%f\n",box[XX][XX],box[YY][YY],box[ZZ][ZZ]); */
309 while (read_next_frame(oenv, status, &fr));
313 gmx_rmpbc_done(gpbc);
318 minx = miny = minz = 0;
325 flp = ffopen("grid.cube", "w");
326 fprintf(flp, "Spatial Distribution Function\n");
327 fprintf(flp, "test\n");
328 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);
329 fprintf(flp, "%5ld%12.6f%12.6f%12.6f\n", maxx-minx+1-(2*iIGNOREOUTER), rBINWIDTH*10./bohr, 0., 0.);
330 fprintf(flp, "%5ld%12.6f%12.6f%12.6f\n", maxy-miny+1-(2*iIGNOREOUTER), 0., rBINWIDTH*10./bohr, 0.);
331 fprintf(flp, "%5ld%12.6f%12.6f%12.6f\n", maxz-minz+1-(2*iIGNOREOUTER), 0., 0., rBINWIDTH*10./bohr);
332 for (i = 0; i < nidxp; i++)
335 if (*(top.atoms.atomname[indexp[i]][0]) == 'C')
339 if (*(top.atoms.atomname[indexp[i]][0]) == 'N')
343 if (*(top.atoms.atomname[indexp[i]][0]) == 'O')
347 if (*(top.atoms.atomname[indexp[i]][0]) == 'H')
351 if (*(top.atoms.atomname[indexp[i]][0]) == 'S')
355 fprintf(flp, "%5d%12.6f%12.6f%12.6f%12.6f\n", v, 0., (double)fr.x[indexp[i]][XX]*10./bohr, (double)fr.x[indexp[i]][YY]*10./bohr, (double)fr.x[indexp[i]][ZZ]*10./bohr);
359 for (k = 0; k < nbin[XX]; k++)
361 if (!(k < minx || k > maxx))
365 for (j = 0; j < nbin[YY]; j++)
367 if (!(j < miny || j > maxy))
371 for (i = 0; i < nbin[ZZ]; i++)
373 if (!(i < minz || i > maxz))
377 if (bin[k][j][i] != 0)
379 printf("A bin was not empty when it should have been empty. Programming error.\n");
380 printf("bin[%d][%d][%d] was = %ld\n", k, j, i, bin[k][j][i]);
389 for (k = 0; k < nbin[XX]; k++)
391 if (k < minx+iIGNOREOUTER || k > maxx-iIGNOREOUTER)
395 for (j = 0; j < nbin[YY]; j++)
397 if (j < miny+iIGNOREOUTER || j > maxy-iIGNOREOUTER)
401 for (i = 0; i < nbin[ZZ]; i++)
403 if (i < minz+iIGNOREOUTER || i > maxz-iIGNOREOUTER)
408 if (bin[k][j][i] > max)
412 if (bin[k][j][i] < min)
420 numcu = (maxx-minx+1-(2*iIGNOREOUTER))*(maxy-miny+1-(2*iIGNOREOUTER))*(maxz-minz+1-(2*iIGNOREOUTER));
423 norm = ((double)numcu*(double)numfr) / (double)tot;
430 for (k = 0; k < nbin[XX]; k++)
432 if (k < minx+iIGNOREOUTER || k > maxx-iIGNOREOUTER)
436 for (j = 0; j < nbin[YY]; j++)
438 if (j < miny+iIGNOREOUTER || j > maxy-iIGNOREOUTER)
442 for (i = 0; i < nbin[ZZ]; i++)
444 if (i < minz+iIGNOREOUTER || i > maxz-iIGNOREOUTER)
448 fprintf(flp, "%12.6f ", norm*(double)bin[k][j][i]/(double)numfr);
456 /* printf("x=%d to %d\n",minx,maxx); */
457 /* printf("y=%d to %d\n",miny,maxy); */
458 /* printf("z=%d to %d\n",minz,maxz); */
462 printf("Counts per frame in all %ld cubes divided by %le\n", numcu, 1.0/norm);
463 printf("Normalized data: average %le, min %le, max %le\n", 1.0, norm*(double)min/(double)numfr, norm*(double)max/(double)numfr);
467 printf("grid.cube contains counts per frame in all %ld cubes\n", numcu);
468 printf("Raw data: average %le, min %le, max %le\n", 1.0/norm, (double)min/(double)numfr, (double)max/(double)numfr);