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48 #include "gmx_fatal.h"
49 #include "chargegroup.h"
52 void calc_chargegroup_radii(const gmx_mtop_t *mtop,rvec *x,
53 real *rvdw1,real *rvdw2,
54 real *rcoul1,real *rcoul2)
56 real r2v1,r2v2,r2c1,r2c2,r2;
57 int ntype,i,j,mb,m,cg,a_mol,a0,a1,a;
70 ntype = mtop->ffparams.atnr;
72 for(i=0; i<ntype; i++)
75 for(j=0; j<ntype; j++)
77 if (mtop->ffparams.iparams[i*ntype+j].lj.c6 != 0 ||
78 mtop->ffparams.iparams[i*ntype+j].lj.c12 != 0)
86 for(mb=0; mb<mtop->nmolblock; mb++)
88 molb = &mtop->molblock[mb];
89 molt = &mtop->moltype[molb->type];
91 atom = molt->atoms.atom;
92 for(m=0; m<molb->nmol; m++)
94 for(cg=0; cg<cgs->nr; cg++)
97 a1 = cgs->index[cg+1];
103 rvec_inc(cen,x[a_mol+a]);
105 svmul(1.0/(a1-a0),cen,cen);
108 r2 = distance2(cen,x[a_mol+a]);
109 if (r2 > r2v2 && (bLJ[atom[a].type ] ||
123 (atom[a].q != 0 || atom[a].qB != 0))
138 a_mol += molb->natoms_mol;
146 *rcoul1 = sqrt(r2c1);
147 *rcoul2 = sqrt(r2c2);
150 void calc_cgcm(FILE *fplog,int cg0,int cg1,t_block *cgs,
151 rvec pos[],rvec cg_cm[])
159 fprintf(fplog,"Calculating centre of geometry for charge groups %d to %d\n",
162 cgindex = cgs->index;
164 /* Compute the center of geometry for all charge groups */
165 for(icg=cg0; (icg<cg1); icg++) {
170 copy_rvec(pos[k0],cg_cm[icg]);
176 for(k=k0; (k<k1); k++) {
177 for(d=0; (d<DIM); d++)
180 for(d=0; (d<DIM); d++)
181 cg_cm[icg][d] = inv_ncg*cg[d];
186 void put_charge_groups_in_box(FILE *fplog,int cg0,int cg1,
187 int ePBC,matrix box,t_block *cgs,
188 rvec pos[],rvec cg_cm[])
191 int npbcdim,icg,k,k0,k1,d,e;
197 if (ePBC == epbcNONE)
198 gmx_incons("Calling put_charge_groups_in_box for a system without PBC");
201 fprintf(fplog,"Putting cgs %d to %d in box\n",cg0,cg1);
203 cgindex = cgs->index;
210 bTric = TRICLINIC(box);
212 for(icg=cg0; (icg<cg1); icg++) {
213 /* First compute the center of geometry for this charge group */
219 copy_rvec(pos[k0],cg_cm[icg]);
224 for(k=k0; (k<k1); k++) {
229 cg_cm[icg][d] = inv_ncg*cg[d];
231 /* Now check pbc for this cg */
233 for(d=npbcdim-1; d>=0; d--) {
234 while(cg_cm[icg][d] < 0) {
235 for(e=d; e>=0; e--) {
236 cg_cm[icg][e] += box[d][e];
237 for(k=k0; (k<k1); k++)
238 pos[k][e] += box[d][e];
241 while(cg_cm[icg][d] >= box[d][d]) {
242 for(e=d; e>=0; e--) {
243 cg_cm[icg][e] -= box[d][e];
244 for(k=k0; (k<k1); k++)
245 pos[k][e] -= box[d][e];
250 for(d=0; d<npbcdim; d++) {
251 while(cg_cm[icg][d] < 0) {
252 cg_cm[icg][d] += box[d][d];
253 for(k=k0; (k<k1); k++)
254 pos[k][d] += box[d][d];
256 while(cg_cm[icg][d] >= box[d][d]) {
257 cg_cm[icg][d] -= box[d][d];
258 for(k=k0; (k<k1); k++)
259 pos[k][d] -= box[d][d];
264 for(d=0; (d<npbcdim); d++) {
265 if ((cg_cm[icg][d] < 0) || (cg_cm[icg][d] >= box[d][d]))
266 gmx_fatal(FARGS,"cg_cm[%d] = %15f %15f %15f\n"
267 "box = %15f %15f %15f\n",
268 icg,cg_cm[icg][XX],cg_cm[icg][YY],cg_cm[icg][ZZ],
269 box[XX][XX],box[YY][YY],box[ZZ][ZZ]);