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43 #include "gmx_fatal.h"
62 static void index_atom2mol(int *n,atom_id *index,t_block *mols)
71 while (index[i] > mols->index[mol]) {
74 gmx_fatal(FARGS,"Atom index out of range: %d",index[i]+1);
76 for(j=mols->index[mol]; j<mols->index[mol+1]; j++) {
77 if (i >= nat || index[i] != j)
78 gmx_fatal(FARGS,"The index group does not consist of whole molecules");
84 fprintf(stderr,"\nSplit group of %d atoms into %d molecules\n",nat,nmol);
89 static void precalc(t_topology top,real normm[]){
94 for(i=0;i<top.mols.nr;i++){
96 l=top.mols.index[i+1];
100 mtot+=top.atoms.atom[j].m;
103 normm[j]=top.atoms.atom[j].m/mtot;
111 int gmx_velacc(int argc,char *argv[])
113 const char *desc[] = {
114 "g_velacc computes the velocity autocorrelation function.",
115 "When the [TT]-m[tt] option is used, the momentum autocorrelation",
116 "function is calculated.[PAR]",
117 "With option [TT]-mol[tt] the velocity autocorrelation function of",
118 "molecules is calculated. In this case the index group should consist",
119 "of molecule numbers instead of atom numbers."
122 static gmx_bool bM=FALSE,bMol=FALSE;
124 { "-m", FALSE, etBOOL, {&bM},
125 "Calculate the momentum autocorrelation function" },
126 { "-mol", FALSE, etBOOL, {&bMol},
127 "Calculate the velocity acf of molecules" }
134 gmx_bool bTPS=FALSE,bTop=FALSE;
141 int teller,n_alloc,i,j,tel3,k,l;
150 { efTRN, "-f", NULL, ffREAD },
151 { efTPS, NULL, NULL, ffOPTRD },
152 { efNDX, NULL, NULL, ffOPTRD },
153 { efXVG, "-o", "vac", ffWRITE }
155 #define NFILE asize(fnm)
159 CopyRight(stderr,argv[0]);
161 ppa = add_acf_pargs(&npargs,pa);
162 parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
163 NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
166 bTPS = bM || ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
169 bTop=read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,NULL,NULL,box,
171 get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
173 rd_index(ftp2fn(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
177 gmx_fatal(FARGS,"Need a topology to determine the molecules");
178 snew(normm,top.atoms.nr);
180 index_atom2mol(&gnx,index,&top.mols);
183 /* Correlation stuff */
185 for(i=0; (i<gnx); i++)
188 read_first_frame(oenv,&status,ftp2fn(efTRN,NFILE,fnm),&fr,TRX_NEED_V);
194 if (teller >= n_alloc) {
197 srenew(c1[i],DIM*n_alloc);
201 for(i=0; i<gnx; i++) {
203 k=top.mols.index[index[i]];
204 l=top.mols.index[index[i]+1];
207 m = top.atoms.atom[j].m;
210 mv_mol[XX] += m*fr.v[j][XX];
211 mv_mol[YY] += m*fr.v[j][YY];
212 mv_mol[ZZ] += m*fr.v[j][ZZ];
214 c1[i][tel3+XX]=mv_mol[XX];
215 c1[i][tel3+YY]=mv_mol[YY];
216 c1[i][tel3+ZZ]=mv_mol[ZZ];
219 for(i=0; i<gnx; i++) {
221 m = top.atoms.atom[index[i]].m;
224 c1[i][tel3+XX]=m*fr.v[index[i]][XX];
225 c1[i][tel3+YY]=m*fr.v[index[i]][YY];
226 c1[i][tel3+ZZ]=m*fr.v[index[i]][ZZ];
232 } while (read_next_frame(oenv,status,&fr));
236 do_autocorr(ftp2fn(efXVG,NFILE,fnm), oenv,
238 "Momentum Autocorrelation Function" :
239 "Velocity Autocorrelation Function",
240 teller,gnx,c1,(t1-t0)/(teller-1),eacVector,TRUE);
242 do_view(oenv,ftp2fn(efXVG,NFILE,fnm),"-nxy");