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56 int gmx_filter(int argc, char *argv[])
58 const char *desc[] = {
59 "[TT]g_filter[tt] performs frequency filtering on a trajectory.",
60 "The filter shape is cos([GRK]pi[grk] t/A) + 1 from -A to +A, where A is given",
61 "by the option [TT]-nf[tt] times the time step in the input trajectory.",
62 "This filter reduces fluctuations with period A by 85%, with period",
63 "2*A by 50% and with period 3*A by 17% for low-pass filtering.",
64 "Both a low-pass and high-pass filtered trajectory can be written.[PAR]",
66 "Option [TT]-ol[tt] writes a low-pass filtered trajectory.",
67 "A frame is written every [TT]-nf[tt] input frames.",
68 "This ratio of filter length and output interval ensures a good",
69 "suppression of aliasing of high-frequency motion, which is useful for",
70 "making smooth movies. Also averages of properties which are linear",
71 "in the coordinates are preserved, since all input frames are weighted",
72 "equally in the output.",
73 "When all frames are needed, use the [TT]-all[tt] option.[PAR]",
75 "Option [TT]-oh[tt] writes a high-pass filtered trajectory.",
76 "The high-pass filtered coordinates are added to the coordinates",
77 "from the structure file. When using high-pass filtering use [TT]-fit[tt]",
78 "or make sure you use a trajectory that has been fitted on",
79 "the coordinates in the structure file."
83 static gmx_bool bNoJump = TRUE, bFit = FALSE, bLowAll = FALSE;
85 { "-nf", FALSE, etINT, {&nf},
86 "Sets the filter length as well as the output interval for low-pass filtering" },
87 { "-all", FALSE, etBOOL, {&bLowAll},
88 "Write all low-pass filtered frames" },
89 { "-nojump", FALSE, etBOOL, {&bNoJump},
90 "Remove jumps of atoms across the box" },
91 { "-fit", FALSE, etBOOL, {&bFit},
92 "Fit all frames to a reference structure" }
94 const char *topfile, *lowfile, *highfile;
95 gmx_bool bTop = FALSE;
99 matrix topbox, *box, boxf;
100 char title[256], *grpname;
105 t_trxstatus *outl, *outh;
106 int nffr, i, fr, nat, j, d, m;
108 real flen, *filt, sum, *t;
109 rvec xcmtop, xcm, **x, *ptr, *xf, *xn, *xp, hbox;
111 gmx_rmpbc_t gpbc = NULL;
113 #define NLEG asize(leg)
115 { efTRX, "-f", NULL, ffREAD },
116 { efTPS, NULL, NULL, ffOPTRD },
117 { efNDX, NULL, NULL, ffOPTRD },
118 { efTRO, "-ol", "lowpass", ffOPTWR },
119 { efTRO, "-oh", "highpass", ffOPTWR }
121 #define NFILE asize(fnm)
123 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
124 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
129 highfile = opt2fn_null("-oh", NFILE, fnm);
132 topfile = ftp2fn(efTPS, NFILE, fnm);
133 lowfile = opt2fn_null("-ol", NFILE, fnm);
137 topfile = ftp2fn_null(efTPS, NFILE, fnm);
138 lowfile = opt2fn("-ol", NFILE, fnm);
142 bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC,
143 &xtop, NULL, topbox, TRUE);
146 gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
147 gmx_rmpbc(gpbc, top.atoms.nr, topbox, xtop);
154 fprintf(stderr, "Select group for least squares fit\n");
155 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
157 snew(w_rls, top.atoms.nr);
158 for (i = 0; i < isize; i++)
160 w_rls[index[i]] = top.atoms.atom[index[i]].m;
162 calc_xcm(xtop, isize, index, top.atoms.atom, xcmtop, FALSE);
163 for (j = 0; j < top.atoms.nr; j++)
165 rvec_dec(xtop[j], xcmtop);
169 /* The actual filter length flen can actually be any real number */
171 /* nffr is the number of frames that we filter over */
175 for (i = 0; i < nffr; i++)
177 filt[i] = cos(2*M_PI*(i - nf + 1)/(real)flen) + 1;
180 fprintf(stdout, "filter weights:");
181 for (i = 0; i < nffr; i++)
184 fprintf(stdout, " %5.3f", filt[i]);
186 fprintf(stdout, "\n");
192 nat = read_first_x(oenv, &in, opt2fn("-f", NFILE, fnm),
193 &(t[nffr - 1]), &(x[nffr - 1]), box[nffr - 1]);
195 for (i = 0; i < nat; i++)
199 /* x[nffr - 1] was already allocated by read_first_x */
200 for (i = 0; i < nffr-1; i++)
207 outl = open_trx(lowfile, "w");
215 outh = open_trx(highfile, "w");
226 if (bNoJump && fr > 0)
229 for (j = 0; j < nat; j++)
231 for (d = 0; d < DIM; d++)
233 hbox[d] = 0.5*box[nffr - 1][d][d];
236 for (i = 0; i < nat; i++)
238 for (m = DIM-1; m >= 0; m--)
242 while (xn[i][m] - xp[i][m] <= -hbox[m])
244 for (d = 0; d <= m; d++)
246 xn[i][d] += box[nffr - 1][m][d];
249 while (xn[i][m] - xp[i][m] > hbox[m])
251 for (d = 0; d <= m; d++)
253 xn[i][d] -= box[nffr - 1][m][d];
262 gmx_rmpbc(gpbc, nat, box[nffr - 1], xn);
266 calc_xcm(xn, isize, index, top.atoms.atom, xcm, FALSE);
267 for (j = 0; j < nat; j++)
269 rvec_dec(xn[j], xcm);
271 do_fit(nat, w_rls, xtop, xn);
272 for (j = 0; j < nat; j++)
274 rvec_inc(xn[j], xcmtop);
277 if (fr >= nffr && (outh || bLowAll || fr % nf == nf - 1))
279 /* Lowpass filtering */
280 for (j = 0; j < nat; j++)
285 for (i = 0; i < nffr; i++)
287 for (j = 0; j < nat; j++)
289 for (d = 0; d < DIM; d++)
291 xf[j][d] += filt[i]*x[i][j][d];
294 for (j = 0; j < DIM; j++)
296 for (d = 0; d < DIM; d++)
298 boxf[j][d] += filt[i]*box[i][j][d];
302 if (outl && (bLowAll || fr % nf == nf - 1))
304 write_trx(outl, nat, ind, topfile ? &(top.atoms) : NULL,
305 0, t[nf - 1], bFit ? topbox : boxf, xf, NULL, NULL);
309 /* Highpass filtering */
310 for (j = 0; j < nat; j++)
312 for (d = 0; d < DIM; d++)
314 xf[j][d] = xtop[j][d] + x[nf - 1][j][d] - xf[j][d];
319 for (j = 0; j < nat; j++)
321 rvec_inc(xf[j], xcmtop);
324 for (j = 0; j < DIM; j++)
326 for (d = 0; d < DIM; d++)
328 boxf[j][d] = topbox[j][d] + box[nf - 1][j][d] - boxf[j][d];
331 write_trx(outh, nat, ind, topfile ? &(top.atoms) : NULL,
332 0, t[nf - 1], bFit ? topbox : boxf, xf, NULL, NULL);
335 /* Cycle all the pointer and the box by one */
337 for (i = 0; i < nffr-1; i++)
341 copy_mat(box[i+1], box[i]);
346 while (read_next_x(oenv, in, &(t[nffr - 1]), x[nffr - 1], box[nffr - 1]));
350 gmx_rmpbc_done(gpbc);