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38 * \brief This file defines functions used by the domdec module
39 * for (bounding) box and pbc information generation.
41 * \author Berk Hess <hess@kth.se>
42 * \ingroup module_domdec
47 #include "gromacs/domdec/domdec.h"
48 #include "gromacs/domdec/domdec_network.h"
49 #include "gromacs/domdec/domdec_struct.h"
50 #include "gromacs/gmxlib/network.h"
51 #include "gromacs/math/functions.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/mdlib/nsgrid.h"
54 #include "gromacs/mdtypes/commrec.h"
55 #include "gromacs/mdtypes/inputrec.h"
56 #include "gromacs/pbcutil/pbc.h"
57 #include "gromacs/utility/fatalerror.h"
59 /*! \brief Calculates the average and standard deviation in 3D of n charge groups */
60 static void calc_cgcm_av_stddev(const t_block *cgs, int n, const rvec *x,
67 int cg, d, k0, k1, k, nrcg;
75 for (cg = 0; cg < n; cg++)
82 copy_rvec(x[k0], cg_cm);
89 for (k = k0; (k < k1); k++)
91 rvec_inc(cg_cm, x[k]);
93 for (d = 0; (d < DIM); d++)
98 for (d = 0; d < DIM; d++)
101 s2[d] += cg_cm[d]*cg_cm[d];
105 if (cr_sum != nullptr)
107 for (d = 0; d < DIM; d++)
113 gmx_sumd(7, buf, cr_sum);
114 for (d = 0; d < DIM; d++)
119 n = (int)(buf[6] + 0.5);
122 dsvmul(1.0/n, s1, s1);
123 dsvmul(1.0/n, s2, s2);
125 for (d = 0; d < DIM; d++)
128 stddev[d] = std::sqrt(s2[d] - s1[d]*s1[d]);
132 /*! \brief Determines if dimensions require triclinic treatment and stores this info in ddbox */
133 static void set_tric_dir(const ivec *dd_nc, gmx_ddbox_t *ddbox, const matrix box)
135 int npbcdim, d, i, j;
137 real dep, inv_skew_fac2;
139 npbcdim = ddbox->npbcdim;
140 normal = ddbox->normal;
141 for (d = 0; d < DIM; d++)
143 ddbox->tric_dir[d] = 0;
144 for (j = d+1; j < npbcdim; j++)
148 ddbox->tric_dir[d] = 1;
149 if (dd_nc != nullptr && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
151 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",
152 (*dd_nc)[XX], (*dd_nc)[YY], (*dd_nc)[ZZ],
153 j+1, box[j][XX], box[j][YY], box[j][ZZ]);
158 /* Construct vectors v for dimension d that are perpendicular
159 * to the triclinic plane of dimension d. Each vector v[i] has
160 * v[i][i]=1 and v[i][d]!=0 for triclinic dimensions, while the third
161 * component is zero. These are used for computing the distance
162 * to a triclinic plane given the distance along dimension d.
163 * Set the trilinic skewing factor that translates
164 * the thickness of a slab perpendicular to this dimension
165 * into the real thickness of the slab.
167 if (ddbox->tric_dir[d])
171 if (d == XX || d == YY)
173 /* Normalize such that the "diagonal" is 1 */
174 svmul(1/box[d+1][d+1], box[d+1], v[d+1]);
175 for (i = 0; i < d; i++)
179 inv_skew_fac2 += gmx::square(v[d+1][d]);
182 /* Normalize such that the "diagonal" is 1 */
183 svmul(1/box[d+2][d+2], box[d+2], v[d+2]);
184 /* Set v[d+2][d+1] to zero by shifting along v[d+1] */
185 dep = v[d+2][d+1]/v[d+1][d+1];
186 for (i = 0; i < DIM; i++)
188 v[d+2][i] -= dep*v[d+1][i];
190 inv_skew_fac2 += gmx::square(v[d+2][d]);
192 cprod(v[d+1], v[d+2], normal[d]);
196 /* cross product with (1,0,0) */
198 normal[d][YY] = v[d+1][ZZ];
199 normal[d][ZZ] = -v[d+1][YY];
203 fprintf(debug, "box[%d] %.3f %.3f %.3f\n",
204 d, box[d][XX], box[d][YY], box[d][ZZ]);
205 for (i = d+1; i < DIM; i++)
207 fprintf(debug, " v[%d] %.3f %.3f %.3f\n",
208 i, v[i][XX], v[i][YY], v[i][ZZ]);
212 ddbox->skew_fac[d] = 1.0/std::sqrt(inv_skew_fac2);
213 /* Set the normal vector length to skew_fac */
214 dep = ddbox->skew_fac[d]/norm(normal[d]);
215 svmul(dep, normal[d], normal[d]);
219 fprintf(debug, "skew_fac[%d] = %f\n", d, ddbox->skew_fac[d]);
220 fprintf(debug, "normal[%d] %.3f %.3f %.3f\n",
221 d, normal[d][XX], normal[d][YY], normal[d][ZZ]);
226 ddbox->skew_fac[d] = 1;
228 for (i = 0; i < DIM; i++)
230 clear_rvec(ddbox->v[d][i]);
231 ddbox->v[d][i][i] = 1;
233 clear_rvec(normal[d]);
239 /*! \brief This function calculates bounding box and pbc info and populates ddbox */
240 static void low_set_ddbox(const t_inputrec *ir, const ivec *dd_nc, const matrix box,
241 gmx_bool bCalcUnboundedSize, int ncg, const t_block *cgs, const rvec *x,
249 ddbox->npbcdim = ePBC2npbcdim(ir->ePBC);
250 ddbox->nboundeddim = inputrec2nboundeddim(ir);
252 for (d = 0; d < ddbox->nboundeddim; d++)
255 ddbox->box_size[d] = box[d][d];
258 if (ddbox->nboundeddim < DIM && bCalcUnboundedSize)
260 calc_cgcm_av_stddev(cgs, ncg, x, av, stddev, cr_sum);
262 /* GRID_STDDEV_FAC * stddev
263 * gives a uniform load for a rectangular block of cg's.
264 * For a sphere it is not a bad approximation for 4x1x1 up to 4x2x2.
266 for (d = ddbox->nboundeddim; d < DIM; d++)
268 b0 = av[d] - GRID_STDDEV_FAC*stddev[d];
269 b1 = av[d] + GRID_STDDEV_FAC*stddev[d];
272 fprintf(debug, "Setting global DD grid boundaries to %f - %f\n",
276 ddbox->box_size[d] = b1 - b0;
280 set_tric_dir(dd_nc, ddbox, box);
283 void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
284 const t_inputrec *ir, const matrix box,
285 gmx_bool bCalcUnboundedSize, const t_block *cgs, const rvec *x,
288 if (!bMasterState || DDMASTER(dd))
290 low_set_ddbox(ir, &dd->nc, box, bCalcUnboundedSize,
291 bMasterState ? cgs->nr : dd->ncg_home, cgs, x,
292 bMasterState ? nullptr : cr_sum,
298 dd_bcast(dd, sizeof(gmx_ddbox_t), ddbox);
302 void set_ddbox_cr(t_commrec *cr, const ivec *dd_nc,
303 const t_inputrec *ir, const matrix box,
304 const t_block *cgs, const rvec *x,
309 low_set_ddbox(ir, dd_nc, box, TRUE, cgs->nr, cgs, x, nullptr, ddbox);
312 gmx_bcast(sizeof(gmx_ddbox_t), ddbox, cr);