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45 #include "domdec_network.h"
49 static void calc_cgcm_av_stddev(t_block *cgs,int n,rvec *x,rvec av,rvec stddev,
55 int cg,d,k0,k1,k,nrcg;
70 copy_rvec(x[k0],cg_cm);
77 for(k=k0; (k<k1); k++)
81 for(d=0; (d<DIM); d++)
89 s2[d] += cg_cm[d]*cg_cm[d];
101 gmx_sumd(7,buf,cr_sum);
107 n = (int)(buf[6] + 0.5);
116 stddev[d] = sqrt(s2[d] - s1[d]*s1[d]);
120 static void set_tric_dir(ivec *dd_nc,gmx_ddbox_t *ddbox,matrix box)
124 real dep,inv_skew_fac2;
126 npbcdim = ddbox->npbcdim;
127 normal = ddbox->normal;
130 ddbox->tric_dir[d] = 0;
131 for(j=d+1; j<npbcdim; j++)
135 ddbox->tric_dir[d] = 1;
136 if (dd_nc != NULL && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
138 gmx_fatal(FARGS,"Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
139 dd_nc[XX],dd_nc[YY],dd_nc[ZZ],
140 j+1,box[j][XX],box[j][YY],box[j][ZZ]);
145 /* Convert box vectors to orthogonal vectors for this dimension,
146 * for use in distance calculations.
147 * Set the trilinic skewing factor that translates
148 * the thickness of a slab perpendicular to this dimension
149 * into the real thickness of the slab.
151 if (ddbox->tric_dir[d])
155 if (d == XX || d == YY)
157 /* Normalize such that the "diagonal" is 1 */
158 svmul(1/box[d+1][d+1],box[d+1],v[d+1]);
163 inv_skew_fac2 += sqr(v[d+1][d]);
166 /* Normalize such that the "diagonal" is 1 */
167 svmul(1/box[d+2][d+2],box[d+2],v[d+2]);
172 /* Make vector [d+2] perpendicular to vector [d+1],
173 * this does not affect the normalization.
175 dep = iprod(v[d+1],v[d+2])/norm2(v[d+1]);
178 v[d+2][i] -= dep*v[d+1][i];
180 inv_skew_fac2 += sqr(v[d+2][d]);
182 cprod(v[d+1],v[d+2],normal[d]);
186 /* cross product with (1,0,0) */
188 normal[d][YY] = v[d+1][ZZ];
189 normal[d][ZZ] = -v[d+1][YY];
193 fprintf(debug,"box[%d] %.3f %.3f %.3f\n",
194 d,box[d][XX],box[d][YY],box[d][ZZ]);
195 for(i=d+1; i<DIM; i++)
197 fprintf(debug," v[%d] %.3f %.3f %.3f\n",
198 i,v[i][XX],v[i][YY],v[i][ZZ]);
202 ddbox->skew_fac[d] = 1.0/sqrt(inv_skew_fac2);
203 /* Set the normal vector length to skew_fac */
204 dep = ddbox->skew_fac[d]/norm(normal[d]);
205 svmul(dep,normal[d],normal[d]);
209 fprintf(debug,"skew_fac[%d] = %f\n",d,ddbox->skew_fac[d]);
210 fprintf(debug,"normal[%d] %.3f %.3f %.3f\n",
211 d,normal[d][XX],normal[d][YY],normal[d][ZZ]);
216 ddbox->skew_fac[d] = 1;
220 clear_rvec(ddbox->v[d][i]);
221 ddbox->v[d][i][i] = 1;
223 clear_rvec(normal[d]);
229 static void low_set_ddbox(t_inputrec *ir,ivec *dd_nc,matrix box,
230 gmx_bool bCalcUnboundedSize,int ncg,t_block *cgs,rvec *x,
238 ddbox->npbcdim = ePBC2npbcdim(ir->ePBC);
239 ddbox->nboundeddim = inputrec2nboundeddim(ir);
241 for(d=0; d<ddbox->nboundeddim; d++)
244 ddbox->box_size[d] = box[d][d];
247 if (ddbox->nboundeddim < DIM && bCalcUnboundedSize)
249 calc_cgcm_av_stddev(cgs,ncg,x,av,stddev,cr_sum);
251 /* GRID_STDDEV_FAC * stddev
252 * gives a uniform load for a rectangular block of cg's.
253 * For a sphere it is not a bad approximation for 4x1x1 up to 4x2x2.
255 for(d=ddbox->nboundeddim; d<DIM; d++)
257 b0 = av[d] - GRID_STDDEV_FAC*stddev[d];
258 b1 = av[d] + GRID_STDDEV_FAC*stddev[d];
261 fprintf(debug,"Setting global DD grid boundaries to %f - %f\n",
265 ddbox->box_size[d] = b1 - b0;
269 set_tric_dir(dd_nc,ddbox,box);
272 void set_ddbox(gmx_domdec_t *dd,gmx_bool bMasterState,t_commrec *cr_sum,
273 t_inputrec *ir,matrix box,
274 gmx_bool bCalcUnboundedSize,t_block *cgs,rvec *x,
277 if (!bMasterState || DDMASTER(dd))
279 low_set_ddbox(ir,&dd->nc,box,bCalcUnboundedSize,
280 bMasterState ? cgs->nr : dd->ncg_home,cgs,x,
281 bMasterState ? NULL : cr_sum,
287 dd_bcast(dd,sizeof(gmx_ddbox_t),ddbox);
291 void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
292 t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
297 low_set_ddbox(ir,dd_nc,box,TRUE,cgs->nr,cgs,x,NULL,ddbox);
300 gmx_bcast(sizeof(gmx_ddbox_t),ddbox,cr);