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57 int gmx_filter(int argc,char *argv[])
59 const char *desc[] = {
60 "[TT]g_filter[tt] performs frequency filtering on a trajectory.",
61 "The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given",
62 "by the option [TT]-nf[tt] times the time step in the input trajectory.",
63 "This filter reduces fluctuations with period A by 85%, with period",
64 "2*A by 50% and with period 3*A by 17% for low-pass filtering.",
65 "Both a low-pass and high-pass filtered trajectory can be written.[PAR]",
67 "Option [TT]-ol[tt] writes a low-pass filtered trajectory.",
68 "A frame is written every [TT]nf[tt] input frames.",
69 "This ratio of filter length and output interval ensures a good",
70 "suppression of aliasing of high-frequency motion, which is useful for",
71 "making smooth movies. Also averages of properties which are linear",
72 "in the coordinates are preserved, since all input frames are weighted",
73 "equally in the output.",
74 "When all frames are needed, use the [TT]-all[tt] option.[PAR]",
76 "Option [TT]-oh[tt] writes a high-pass filtered trajectory.",
77 "The high-pass filtered coordinates are added to the coordinates",
78 "from the structure file. When using high-pass filtering use [TT]-fit[tt]",
79 "or make sure you use a trajectory which has been fitted on",
80 "the coordinates in the structure file."
84 static gmx_bool bNoJump = TRUE,bFit = FALSE,bLowAll = FALSE;
86 { "-nf", FALSE, etINT, {&nf},
87 "Sets the filter length as well as the output interval for low-pass filtering" },
88 { "-all", FALSE, etBOOL, {&bLowAll},
89 "Write all low-pass filtered frames" },
90 { "-nojump", FALSE, etBOOL, {&bNoJump},
91 "Remove jumps of atoms across the box" },
92 { "-fit", FALSE, etBOOL, {&bFit},
93 "Fit all frames to a reference structure" }
95 const char *topfile,*lowfile,*highfile;
100 matrix topbox,*box,boxf;
101 char title[256],*grpname;
106 t_trxstatus *outl,*outh;
107 int nffr,i,fr,nat,j,d,m;
109 real flen,*filt,sum,*t;
110 rvec xcmtop,xcm,**x,*ptr,*xf,*xn,*xp,hbox;
112 gmx_rmpbc_t gpbc=NULL;
114 #define NLEG asize(leg)
116 { efTRX, "-f", NULL, ffREAD },
117 { efTPS, NULL, NULL, ffOPTRD },
118 { efNDX, NULL, NULL, ffOPTRD },
119 { efTRO, "-ol", "lowpass", ffOPTWR },
120 { efTRO, "-oh", "highpass", ffOPTWR }
122 #define NFILE asize(fnm)
124 CopyRight(stderr,argv[0]);
125 parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
126 NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
128 highfile = opt2fn_null("-oh",NFILE,fnm);
130 topfile = ftp2fn(efTPS,NFILE,fnm);
131 lowfile = opt2fn_null("-ol",NFILE,fnm);
133 topfile = ftp2fn_null(efTPS,NFILE,fnm);
134 lowfile = opt2fn("-ol",NFILE,fnm);
137 bTop = read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,
138 &xtop,NULL,topbox,TRUE);
140 gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,topbox);
141 gmx_rmpbc(gpbc,top.atoms.nr,topbox,xtop);
147 fprintf(stderr,"Select group for least squares fit\n");
148 get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
150 snew(w_rls,top.atoms.nr);
151 for(i=0; i<isize; i++)
152 w_rls[index[i]] = top.atoms.atom[index[i]].m;
153 calc_xcm(xtop,isize,index,top.atoms.atom,xcmtop,FALSE);
154 for(j=0; j<top.atoms.nr; j++)
155 rvec_dec(xtop[j],xcmtop);
158 /* The actual filter length flen can actually be any real number */
160 /* nffr is the number of frames that we filter over */
164 for(i=0; i<nffr; i++) {
165 filt[i] = cos(2*M_PI*(i - nf + 1)/(real)flen) + 1;
168 fprintf(stdout,"filter weights:");
169 for(i=0; i<nffr; i++) {
171 fprintf(stdout," %5.3f",filt[i]);
173 fprintf(stdout,"\n");
179 nat = read_first_x(oenv,&in,opt2fn("-f",NFILE,fnm),
180 &(t[nffr - 1]),&(x[nffr - 1]),box[nffr - 1]);
184 /* x[nffr - 1] was already allocated by read_first_x */
185 for(i=0; i<nffr-1; i++)
189 outl = open_trx(lowfile,"w");
193 outh = open_trx(highfile,"w");
200 if (bNoJump && fr > 0) {
204 hbox[d] = 0.5*box[nffr - 1][d][d];
206 for(m=DIM-1; m>=0; m--)
208 while (xn[i][m] - xp[i][m] <= -hbox[m])
210 xn[i][d] += box[nffr - 1][m][d];
211 while (xn[i][m] - xp[i][m] > hbox[m])
213 xn[i][d] -= box[nffr - 1][m][d];
217 gmx_rmpbc(gpbc,nat,box[nffr - 1],xn);
220 calc_xcm(xn,isize,index,top.atoms.atom,xcm,FALSE);
223 do_fit(nat,w_rls,xtop,xn);
225 rvec_inc(xn[j],xcmtop);
227 if (fr >= nffr && (outh || bLowAll || fr % nf == nf - 1)) {
228 /* Lowpass filtering */
232 for(i=0; i<nffr; i++) {
235 xf[j][d] += filt[i]*x[i][j][d];
238 boxf[j][d] += filt[i]*box[i][j][d];
240 if (outl && (bLowAll || fr % nf == nf - 1))
241 write_trx(outl,nat,ind,topfile ? &(top.atoms) : NULL,
242 0,t[nf - 1],bFit ? topbox : boxf,xf,NULL,NULL);
244 /* Highpass filtering */
247 xf[j][d] = xtop[j][d] + x[nf - 1][j][d] - xf[j][d];
250 rvec_inc(xf[j],xcmtop);
253 boxf[j][d] = topbox[j][d] + box[nf - 1][j][d] - boxf[j][d];
254 write_trx(outh,nat,ind,topfile ? &(top.atoms) : NULL,
255 0,t[nf - 1],bFit ? topbox : boxf,xf,NULL,NULL);
258 /* Cycle all the pointer and the box by one */
260 for(i=0; i<nffr-1; i++) {
263 copy_mat(box[i+1],box[i]);
267 } while (read_next_x(oenv,in,&(t[nffr - 1]),nat,x[nffr - 1],box[nffr - 1]));
270 gmx_rmpbc_done(gpbc);