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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
);