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33 * GROwing Monsters And Cloning Shrimps
35 /* This file is completely threadsafe - keep it that way! */
47 #include "gmx_fatal.h"
54 #define header "Neighborlist:"
56 static void write_nblist(FILE *out,gmx_domdec_t *dd,t_nblist *nblist,int nDNL)
58 int i,nii,ii,j,zi,zj0,zj1,aj,zj,nj;
59 int ca1[DD_MAXZONE],np[DD_MAXZONE];
60 gmx_domdec_zones_t *dd_zones;
62 if (nblist->nri > 0) {
63 fprintf(out,"il_name: %s Solvent opt: %s\n",
64 nrnb_str(nblist->il_code),
65 enlist_names[nblist->enlist]);
66 fprintf(out,"nri: %d npair: %d\n",nblist->nri,nblist->nrj);
68 dd_zones = domdec_zones(dd);
70 for(zi=0; zi<dd_zones->n; zi++)
71 ca1[zi] = dd->cgindex[dd_zones->cg_range[zi+1]];
73 for(zi=0; zi<dd_zones->nizone; zi++) {
74 zj0 = dd_zones->izone[zi].j0;
75 zj1 = dd_zones->izone[zi].j1;
76 for(zj=zj0; zj<zj1; zj++)
78 while(i < nblist->nri && nblist->iinr[i] < ca1[zi]) {
79 for(j=nblist->jindex[i]; (j<nblist->jindex[i+1]); j++) {
88 fprintf(out,"DD zone %d:",zi);
89 for(zj=zj0; zj<zj1; zj++)
90 fprintf(out," %d %d",zj,np[zj]);
95 for(i=0; i<nblist->nri; i++) {
97 if (nDNL >= 3 && nblist->enlist != enlistATOM_ATOM)
99 nj = nblist->jindex[i+1] - nblist->jindex[i];
100 fprintf(out,"i: %d shift: %d gid: %d nj: %d\n",
101 ddglatnr(dd,nblist->iinr[i]),
102 nblist->shift[i],nblist->gid[i],nj);
103 for(ii=0; ii<nii; ii++) {
104 for(j=nblist->jindex[i]; (j<nblist->jindex[i+1]); j++) {
105 fprintf(out," i: %5d j: %5d\n",
106 ddglatnr(dd,nblist->iinr[i]+ii),
107 ddglatnr(dd,nblist->jjnr[j]));
116 static void set_mat(FILE *fp,int **mat,int i0,int ni,int j0,int nj,
117 gmx_bool bSymm,int shift)
121 for(i=i0; (i<i0+ni); i++) {
122 for(j=j0; (j<j0+nj); j++) {
124 fprintf(fp,"mat[%d][%d] changing from %d to %d\n",
125 i,j,mat[i][j],shift+1);
128 mat[j][i] = 27-shift;
133 int read_nblist(FILE *in,FILE *fp,int **mat,int natoms,gmx_bool bSymm)
136 char buf[256],b1[32],b2[32],solv[256],il_code[256];
137 int i,ii,j,nnbl,full,icmp,nri,isolv;
138 int iatom,nrj,nj,shift,gid,nargs,njtot=0;
141 if (fgets2(buf,255,in) == NULL)
142 gmx_fatal(FARGS,"EOF when looking for '%s' in logfile",header);
143 } while (strstr(buf,header) == NULL);
147 if (fgets2(buf,255,in) == NULL)
149 } while (strstr(buf,"nri:") == NULL);
152 if ((nargs = sscanf(buf,"%*s%s%*s%s",il_code,solv)) != 2) {
153 fprintf(stderr,"Can not find the right il_code\n");
156 for(isolv=0; (isolv<esolNR); isolv++)
157 if (strstr(esol_names[isolv],solv) != NULL)
160 if (isolv == esolNR) {
161 fprintf(stderr,"Can not read il_code or solv (nargs=%d)\n",nargs);
166 isolv = enlistATOM_ATOM;
168 /* gmx_fatal(FARGS,"Can not read il_code or solv (nargs=%d)",nargs);*/
169 if ((nargs = sscanf(buf,"%*s%d%*s%d",&nri,&nrj)) != 2)
170 gmx_fatal(FARGS,"Can not read nri or nrj (nargs=%d)",nargs);
171 for(ii=0; (ii<nri); ii++) {
172 if ((nargs = fscanf(in,"%*s%d%*s%d%*s%d%*s%d",
173 &iatom,&shift,&gid,&nj)) != 4)
174 gmx_fatal(FARGS,"Can not read iatom, shift gid or nj (nargs=%d)",nargs);
175 /* Number shifts from 1 to 27 iso 0 to 26 to distinguish uninitialized
178 range_check(iatom,0,natoms);
179 for(i=0; (i<nj); i++) {
180 if ((nargs = fscanf(in,"%*s%d",&j)) != 1)
181 gmx_fatal(FARGS,"Can not read j");
182 range_check(j,0,natoms);
184 case enlistATOM_ATOM:
185 set_mat(fp,mat,iatom,1,j,1,bSymm,shift);
189 set_mat(fp,mat,iatom,3,j,1,bSymm,shift);
193 set_mat(fp,mat,iatom,3,j,3,bSymm,shift);
196 case enlistTIP4P_ATOM:
197 set_mat(fp,mat,iatom,4,j,1,bSymm,shift);
200 case enlistTIP4P_TIP4P:
201 set_mat(fp,mat,iatom,4,j,4,bSymm,shift);
205 gmx_incons("non-existing solvent type");
209 fprintf(fp,"nri = %d nrj = %d\n",nri,nrj);
214 void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL)
217 static FILE *fp=NULL;
223 sprintf(buf,"nlist_n%d.txt",cr->nodeid);
225 sprintf(buf,"nlist.txt");
227 fp = gmx_fio_fopen(buf,"w");
229 fprintf(fp,"%s\n",header);
231 for(n=0; (n<fr->nnblists); n++)
232 for(i=0; (i<eNL_NR); i++)
233 write_nblist(fp,cr->dd,&fr->nblists[n].nlist_sr[i],nDNL);
238 fprintf(out,"%s\n",header);
240 for(n=0; (n<fr->nnblists); n++)
241 for(i=0; (i<eNL_NR); i++)
242 write_nblist(out,cr->dd,&fr->nblists[n].nlist_sr[i],nDNL);