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58 #define EPS0 8.85419E-12
59 #define ELC 1.60219E-19
61 /****************************************************************************/
62 /* This program calculates the electrostatic potential across the box by */
63 /* determining the charge density in slices of the box and integrating these*/
65 /* Peter Tieleman, April 1995 */
66 /* It now also calculates electrostatic potential in spherical micelles, */
67 /* using \frac{1}{r}\frac{d^2r\Psi}{r^2} = - \frac{\rho}{\epsilon_0} */
68 /* This probably sucks but it seems to work. */
69 /****************************************************************************/
71 static int ce = 0, cb = 0;
73 /* this routine integrates the array data and returns the resulting array */
74 /* routine uses simple trapezoid rule */
75 void p_integrate(double *result, double data[], int ndata, double slWidth)
82 fprintf(stderr, "Warning: nr of slices very small. This will result"
86 fprintf(stderr, "Integrating from slice %d to slice %d\n", cb, ndata-ce);
88 for (slice = cb; slice < (ndata-ce); slice++)
91 for (i = cb; i < slice; i++)
93 sum += slWidth * (data[i] + 0.5 * (data[i+1] - data[i]));
100 void calc_potential(const char *fn, atom_id **index, int gnx[],
101 double ***slPotential, double ***slCharge,
102 double ***slField, int *nslices,
103 t_topology *top, int ePBC,
104 int axis, int nr_grps, double *slWidth,
105 double fudge_z, gmx_bool bSpherical, gmx_bool bCorrect,
106 const output_env_t oenv)
108 rvec *x0; /* coordinates without pbc */
109 matrix box; /* box (3x3) */
110 int natoms; /* nr. atoms in trj */
112 int **slCount, /* nr. of atoms in one slice for a group */
113 i, j, n, /* loop indices */
116 nr_frames = 0, /* number of frames */
117 slice; /* current slice */
118 double slVolume; /* volume of slice for spherical averaging */
123 gmx_rmpbc_t gpbc = NULL;
137 gmx_fatal(FARGS, "Invalid axes. Terminating\n");
140 if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
142 gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
147 *nslices = (int)(box[axis][axis] * 10); /* default value */
150 fprintf(stderr, "\nDividing the box in %d slices\n", *nslices);
152 snew(*slField, nr_grps);
153 snew(*slCharge, nr_grps);
154 snew(*slPotential, nr_grps);
156 for (i = 0; i < nr_grps; i++)
158 snew((*slField)[i], *nslices);
159 snew((*slCharge)[i], *nslices);
160 snew((*slPotential)[i], *nslices);
164 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
166 /*********** Start processing trajectory ***********/
169 *slWidth = box[axis][axis]/(*nslices);
171 gmx_rmpbc(gpbc, natoms, box, x0);
173 /* calculate position of center of mass based on group 1 */
174 calc_xcm(x0, gnx[0], index[0], top->atoms.atom, xcm, FALSE);
177 for (n = 0; n < nr_grps; n++)
179 /* Check whether we actually have all positions of the requested index
180 * group in the trajectory file */
183 gmx_fatal(FARGS, "You selected a group with %d atoms, but only %d atoms\n"
184 "were found in the trajectory.\n", gnx[n], natoms);
186 for (i = 0; i < gnx[n]; i++) /* loop over all atoms in index file */
190 rvec_add(x0[index[n][i]], xcm, x0[index[n][i]]);
191 /* only distance from origin counts, not sign */
192 slice = norm(x0[index[n][i]])/(*slWidth);
194 /* this is a nice check for spherical groups but not for
195 all water in a cubic box since a lot will fall outside
197 if (slice > (*nslices))
199 fprintf(stderr,"Warning: slice = %d\n",slice);
202 (*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
206 z = x0[index[n][i]][axis];
210 z += box[axis][axis];
212 if (z > box[axis][axis])
214 z -= box[axis][axis];
216 /* determine which slice atom is in */
217 slice = (z / (*slWidth));
218 (*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
224 while (read_next_x(oenv, status, &t, x0, box));
226 gmx_rmpbc_done(gpbc);
228 /*********** done with status file **********/
231 /* slCharge now contains the total charge per slice, summed over all
232 frames. Now divide by nr_frames and integrate twice
238 fprintf(stderr, "\n\nRead %d frames from trajectory. Calculating potential"
239 "in spherical coordinates\n", nr_frames);
243 fprintf(stderr, "\n\nRead %d frames from trajectory. Calculating potential\n",
247 for (n = 0; n < nr_grps; n++)
249 for (i = 0; i < *nslices; i++)
253 /* charge per volume is now the summed charge, divided by the nr
254 of frames and by the volume of the slice it's in, 4pi r^2 dr
256 slVolume = 4*M_PI * sqr(i) * sqr(*slWidth) * *slWidth;
259 (*slCharge)[n][i] = 0;
263 (*slCharge)[n][i] = (*slCharge)[n][i] / (nr_frames * slVolume);
268 /* get charge per volume */
269 (*slCharge)[n][i] = (*slCharge)[n][i] * (*nslices) /
270 (nr_frames * box[axis][axis] * box[ax1][ax1] * box[ax2][ax2]);
273 /* Now we have charge densities */
276 if (bCorrect && !bSpherical)
278 for (n = 0; n < nr_grps; n++)
282 for (i = 0; i < *nslices; i++)
284 if (fabs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
287 qsum += (*slCharge)[n][i];
291 for (i = 0; i < *nslices; i++)
293 if (fabs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
295 (*slCharge)[n][i] -= qsum;
301 for (n = 0; n < nr_grps; n++)
303 /* integrate twice to get field and potential */
304 p_integrate((*slField)[n], (*slCharge)[n], *nslices, *slWidth);
308 if (bCorrect && !bSpherical)
310 for (n = 0; n < nr_grps; n++)
314 for (i = 0; i < *nslices; i++)
316 if (fabs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
319 qsum += (*slField)[n][i];
323 for (i = 0; i < *nslices; i++)
325 if (fabs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
327 (*slField)[n][i] -= qsum;
333 for (n = 0; n < nr_grps; n++)
335 p_integrate((*slPotential)[n], (*slField)[n], *nslices, *slWidth);
338 /* Now correct for eps0 and in spherical case for r*/
339 for (n = 0; n < nr_grps; n++)
341 for (i = 0; i < *nslices; i++)
345 (*slPotential)[n][i] = ELC * (*slPotential)[n][i] * -1.0E9 /
346 (EPS0 * i * (*slWidth));
347 (*slField)[n][i] = ELC * (*slField)[n][i] * 1E18 /
348 (EPS0 * i * (*slWidth));
352 (*slPotential)[n][i] = ELC * (*slPotential)[n][i] * -1.0E9 / EPS0;
353 (*slField)[n][i] = ELC * (*slField)[n][i] * 1E18 / EPS0;
358 sfree(x0); /* free memory used by coordinate array */
361 void plot_potential(double *potential[], double *charge[], double *field[],
362 const char *afile, const char *bfile, const char *cfile,
363 int nslices, int nr_grps, const char *grpname[], double slWidth,
364 const output_env_t oenv)
366 FILE *pot, /* xvgr file with potential */
367 *cha, /* xvgr file with charges */
368 *fie; /* xvgr files with fields */
369 char buf[256]; /* for xvgr title */
372 sprintf(buf, "Electrostatic Potential");
373 pot = xvgropen(afile, buf, "Box (nm)", "Potential (V)", oenv);
374 xvgr_legend(pot, nr_grps, grpname, oenv);
376 sprintf(buf, "Charge Distribution");
377 cha = xvgropen(bfile, buf, "Box (nm)", "Charge density (q/nm\\S3\\N)", oenv);
378 xvgr_legend(cha, nr_grps, grpname, oenv);
380 sprintf(buf, "Electric Field");
381 fie = xvgropen(cfile, buf, "Box (nm)", "Field (V/nm)", oenv);
382 xvgr_legend(fie, nr_grps, grpname, oenv);
384 for (slice = cb; slice < (nslices - ce); slice++)
386 fprintf(pot, "%20.16g ", slice * slWidth);
387 fprintf(cha, "%20.16g ", slice * slWidth);
388 fprintf(fie, "%20.16g ", slice * slWidth);
389 for (n = 0; n < nr_grps; n++)
391 fprintf(pot, " %20.16g", potential[n][slice]);
392 fprintf(fie, " %20.16g", field[n][slice]/1e9); /* convert to V/nm */
393 fprintf(cha, " %20.16g", charge[n][slice]);
405 int gmx_potential(int argc, char *argv[])
407 const char *desc[] = {
408 "[TT]g_potential[tt] computes the electrostatical potential across the box. The potential is",
409 "calculated by first summing the charges per slice and then integrating",
410 "twice of this charge distribution. Periodic boundaries are not taken",
411 "into account. Reference of potential is taken to be the left side of",
412 "the box. It is also possible to calculate the potential in spherical",
413 "coordinates as function of r by calculating a charge distribution in",
414 "spherical slices and twice integrating them. epsilon_r is taken as 1,",
415 "but 2 is more appropriate in many cases."
418 static int axis = 2; /* normal to memb. default z */
419 static const char *axtitle = "Z";
420 static int nslices = 10; /* nr of slices defined */
421 static int ngrps = 1;
422 static gmx_bool bSpherical = FALSE; /* default is bilayer types */
423 static real fudge_z = 0; /* translate coordinates */
424 static gmx_bool bCorrect = 0;
426 { "-d", FALSE, etSTR, {&axtitle},
427 "Take the normal on the membrane in direction X, Y or Z." },
428 { "-sl", FALSE, etINT, {&nslices},
429 "Calculate potential as function of boxlength, dividing the box"
430 " in this number of slices." },
431 { "-cb", FALSE, etINT, {&cb},
432 "Discard this number of first slices of box for integration" },
433 { "-ce", FALSE, etINT, {&ce},
434 "Discard this number of last slices of box for integration" },
435 { "-tz", FALSE, etREAL, {&fudge_z},
436 "Translate all coordinates by this distance in the direction of the box" },
437 { "-spherical", FALSE, etBOOL, {&bSpherical},
438 "Calculate spherical thingie" },
439 { "-ng", FALSE, etINT, {&ngrps},
440 "Number of groups to consider" },
441 { "-correct", FALSE, etBOOL, {&bCorrect},
442 "Assume net zero charge of groups to improve accuracy" }
444 const char *bugs[] = {
445 "Discarding slices for integration should not be necessary."
448 double **potential, /* potential per slice */
449 **charge, /* total charge per slice */
450 **field, /* field per slice */
451 slWidth; /* width of one slice */
452 char **grpname; /* groupnames */
453 int *ngx; /* sizes of groups */
454 t_topology *top; /* topology */
456 atom_id **index; /* indices for all groups */
457 t_filenm fnm[] = { /* files for g_order */
458 { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
459 { efNDX, NULL, NULL, ffREAD }, /* index file */
460 { efTPX, NULL, NULL, ffREAD }, /* topology file */
461 { efXVG, "-o", "potential", ffWRITE }, /* xvgr output file */
462 { efXVG, "-oc", "charge", ffWRITE }, /* xvgr output file */
463 { efXVG, "-of", "field", ffWRITE }, /* xvgr output file */
466 #define NFILE asize(fnm)
468 parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
469 NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
473 axis = toupper(axtitle[0]) - 'X';
475 top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
477 snew(grpname, ngrps);
481 rd_index(ftp2fn(efNDX, NFILE, fnm), ngrps, ngx, index, grpname);
484 calc_potential(ftp2fn(efTRX, NFILE, fnm), index, ngx,
485 &potential, &charge, &field,
486 &nslices, top, ePBC, axis, ngrps, &slWidth, fudge_z,
487 bSpherical, bCorrect, oenv);
489 plot_potential(potential, charge, field, opt2fn("-o", NFILE, fnm),
490 opt2fn("-oc", NFILE, fnm), opt2fn("-of", NFILE, fnm),
491 nslices, ngrps, (const char**)grpname, slWidth, oenv);
493 do_view(oenv, opt2fn("-o", NFILE, fnm), NULL); /* view xvgr file */
494 do_view(oenv, opt2fn("-oc", NFILE, fnm), NULL); /* view xvgr file */
495 do_view(oenv, opt2fn("-of", NFILE, fnm), NULL); /* view xvgr file */