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45 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/fileio/xvgr.h"
53 #include "gromacs/utility/futil.h"
54 #include "gromacs/commandline/pargs.h"
57 #include "gromacs/fileio/trxio.h"
59 #include "gromacs/utility/fatalerror.h"
61 /****************************************************************************/
62 /* This program calculates the ordering of water molecules across a box, as */
63 /* function of the z-coordinate. This implies averaging over slices and over*/
64 /* time. Output is the average cos of the angle of the dipole with the */
65 /* normal, per slice. */
66 /* In addition, it calculates the average dipole moment itself in three */
68 /****************************************************************************/
70 void calc_h2order(const char *fn, atom_id index[], int ngx, rvec **slDipole,
71 real **slOrder, real *slWidth, int *nslices,
72 t_topology *top, int ePBC,
73 int axis, gmx_bool bMicel, atom_id micel[], int nmic,
74 const output_env_t oenv)
76 rvec *x0, /* coordinates with pbc */
77 dipole, /* dipole moment due to one molecules */
79 com; /* center of mass of micel, with bMicel */
80 rvec *dip; /* sum of dipoles, unnormalized */
81 matrix box; /* box (3x3) */
83 real t, /* time from trajectory */
84 *sum, /* sum of all cosines of dipoles, per slice */
85 *frame; /* order over one frame */
86 int natoms, /* nr. atoms in trj */
88 slice = 0, /* current slice number */
89 *count; /* nr. of atoms in one slice */
90 gmx_rmpbc_t gpbc = NULL;
92 if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
94 gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
99 *nslices = (int)(box[axis][axis] * 10); /* default value */
106 normal[0] = 1; normal[1] = 0; normal[2] = 0;
109 normal[0] = 0; normal[1] = 1; normal[2] = 0;
112 normal[0] = 0; normal[1] = 0; normal[2] = 1;
115 gmx_fatal(FARGS, "No valid value for -axis-. Exiting.\n");
116 /* make compiler happy */
117 normal[0] = 1; normal[1] = 0; normal[2] = 0;
121 snew(count, *nslices);
124 snew(frame, *nslices);
126 *slWidth = box[axis][axis]/(*nslices);
127 fprintf(stderr, "Box divided in %d slices. Initial width of slice: %f\n",
132 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
133 /*********** Start processing trajectory ***********/
136 *slWidth = box[axis][axis]/(*nslices);
139 gmx_rmpbc(gpbc, natoms, box, x0);
143 calc_xcm(x0, nmic, micel, top->atoms.atom, com, FALSE);
146 for (i = 0; i < ngx/3; i++)
148 /* put all waters in box */
149 for (j = 0; j < DIM; j++)
151 if (x0[index[3*i]][j] < 0)
153 x0[index[3*i]][j] += box[j][j];
154 x0[index[3*i+1]][j] += box[j][j];
155 x0[index[3*i+2]][j] += box[j][j];
157 if (x0[index[3*i]][j] > box[j][j])
159 x0[index[3*i]][j] -= box[j][j];
160 x0[index[3*i+1]][j] -= box[j][j];
161 x0[index[3*i+2]][j] -= box[j][j];
165 for (j = 0; j < DIM; j++)
168 x0[index[3*i]][j] * top->atoms.atom[index[3*i]].q +
169 x0[index[3*i+1]][j] * top->atoms.atom[index[3*i+1]].q +
170 x0[index[3*i+2]][j] * top->atoms.atom[index[3*i+2]].q;
173 /* now we have a dipole vector. Might as well safe it. Then the
174 rest depends on whether we're dealing with
175 a flat or a spherical interface.
179 { /* this is for spherical interfaces */
180 rvec_sub(com, x0[index[3*i]], normal); /* vector from Oxygen to COM */
181 slice = norm(normal)/(*slWidth); /* spherical slice */
183 sum[slice] += iprod(dipole, normal) / (norm(dipole) * norm(normal));
184 frame[slice] += iprod(dipole, normal) / (norm(dipole) * norm(normal));
190 /* this is for flat interfaces */
192 /* determine which slice atom is in */
193 slice = (x0[index[3*i]][axis] / (*slWidth));
194 if (slice < 0 || slice >= *nslices)
196 fprintf(stderr, "Coordinate: %f ", x0[index[3*i]][axis]);
197 fprintf(stderr, "HELP PANIC! slice = %d, OUT OF RANGE!\n", slice);
201 rvec_add(dipole, dip[slice], dip[slice]);
202 /* Add dipole to total. mag[slice] is total dipole in axis direction */
203 sum[slice] += iprod(dipole, normal)/norm(dipole);
204 frame[slice] += iprod(dipole, normal)/norm(dipole);
205 /* increase count for that slice */
212 while (read_next_x(oenv, status, &t, x0, box));
213 /*********** done with status file **********/
215 fprintf(stderr, "\nRead trajectory. Printing parameters to file\n");
216 gmx_rmpbc_done(gpbc);
218 for (i = 0; i < *nslices; i++) /* average over frames */
220 fprintf(stderr, "%d waters in slice %d\n", count[i], i);
221 if (count[i] > 0) /* divide by number of molecules in each slice */
223 sum[i] = sum[i] / count[i];
224 dip[i][XX] = dip[i][XX] / count[i];
225 dip[i][YY] = dip[i][YY] / count[i];
226 dip[i][ZZ] = dip[i][ZZ] / count[i];
230 fprintf(stderr, "No water in slice %d\n", i);
234 *slOrder = sum; /* copy a pointer, I hope */
236 sfree(x0); /* free memory used by coordinate arrays */
239 void h2order_plot(rvec dipole[], real order[], const char *afile,
240 int nslices, real slWidth, const output_env_t oenv)
242 FILE *ord; /* xvgr files with order parameters */
243 int slice; /* loop index */
244 char buf[256]; /* for xvgr title */
245 real factor; /* conversion to Debye from electron*nm */
247 /* factor = 1e-9*1.60217733e-19/3.336e-30 */
248 factor = 1.60217733/3.336e-2;
249 fprintf(stderr, "%d slices\n", nslices);
250 sprintf(buf, "Water orientation with respect to normal");
251 ord = xvgropen(afile, buf,
252 "box (nm)", "mu_x, mu_y, mu_z (D), cosine with normal", oenv);
254 for (slice = 0; slice < nslices; slice++)
256 fprintf(ord, "%8.3f %8.3f %8.3f %8.3f %e\n", slWidth*slice,
257 factor*dipole[slice][XX], factor*dipole[slice][YY],
258 factor*dipole[slice][ZZ], order[slice]);
264 int gmx_h2order(int argc, char *argv[])
266 const char *desc[] = {
267 "[THISMODULE] computes the orientation of water molecules with respect to the normal",
268 "of the box. The program determines the average cosine of the angle",
269 "between the dipole moment of water and an axis of the box. The box is",
270 "divided in slices and the average orientation per slice is printed.",
271 "Each water molecule is assigned to a slice, per time frame, based on the",
272 "position of the oxygen. When [TT]-nm[tt] is used, the angle between the water",
273 "dipole and the axis from the center of mass to the oxygen is calculated",
274 "instead of the angle between the dipole and a box axis."
276 static int axis = 2; /* normal to memb. default z */
277 static const char *axtitle = "Z";
278 static int nslices = 0; /* nr of slices defined */
280 { "-d", FALSE, etSTR, {&axtitle},
281 "Take the normal on the membrane in direction X, Y or Z." },
282 { "-sl", FALSE, etINT, {&nslices},
283 "Calculate order parameter as function of boxlength, dividing the box"
284 " in this number of slices."}
286 const char *bugs[] = {
287 "The program assigns whole water molecules to a slice, based on the first "
288 "atom of three in the index file group. It assumes an order O,H,H. "
289 "Name is not important, but the order is. If this demand is not met, "
290 "assigning molecules to slices is different."
294 real *slOrder, /* av. cosine, per slice */
295 slWidth = 0.0; /* width of a slice */
297 char *grpname, /* groupnames */
299 int ngx, /* nr. of atomsin sol group */
300 nmic = 0; /* nr. of atoms in micelle */
301 t_topology *top; /* topology */
303 atom_id *index, /* indices for solvent group */
305 gmx_bool bMicel = FALSE; /* think we're a micel */
306 t_filenm fnm[] = { /* files for g_order */
307 { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
308 { efNDX, NULL, NULL, ffREAD }, /* index file */
309 { efNDX, "-nm", NULL, ffOPTRD }, /* index with micelle atoms */
310 { efTPX, NULL, NULL, ffREAD }, /* topology file */
311 { efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
314 #define NFILE asize(fnm)
316 if (!parse_common_args(&argc, argv,
317 PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
318 fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
322 bMicel = opt2bSet("-nm", NFILE, fnm);
324 top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
326 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);
330 rd_index(opt2fn("-nm", NFILE, fnm), 1, &nmic, &micelle, &micname);
333 calc_h2order(ftp2fn(efTRX, NFILE, fnm), index, ngx, &slDipole, &slOrder,
334 &slWidth, &nslices, top, ePBC, axis, bMicel, micelle, nmic,
337 h2order_plot(slDipole, slOrder, opt2fn("-o", NFILE, fnm), nslices,
340 do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy"); /* view xvgr file */