1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This file is part of Gromacs Copyright (c) 1991-2008
5 * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
7 * This program is free software; you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation; either version 2
10 * of the License, or (at your option) any later version.
12 * To help us fund GROMACS development, we humbly ask that you cite
13 * the research papers on the package. Check out http://www.gromacs.org
16 * Gnomes, ROck Monsters And Chili Sauce
21 #include "visibility.h"
23 #include "types/commrec.h"
31 int ddglatnr(gmx_domdec_t
*dd
,int i
);
32 /* Returns the global topology atom number belonging to local atom index i.
33 * This function is intended for writing ascii output
34 * and returns atom numbers starting at 1.
35 * When dd=NULL returns i+1.
38 t_block
*dd_charge_groups_global(gmx_domdec_t
*dd
);
39 /* Return a block struct for the charge groups of the whole system */
41 gmx_bool
dd_filled_nsgrid_home(gmx_domdec_t
*dd
);
42 /* Is the ns grid already filled with the home particles? */
44 void dd_store_state(gmx_domdec_t
*dd
,t_state
*state
);
45 /* Store the global cg indices of the home cgs in state,
46 * so it can be reset, even after a new DD partitioning.
49 gmx_domdec_zones_t
*domdec_zones(gmx_domdec_t
*dd
);
51 void dd_get_ns_ranges(gmx_domdec_t
*dd
,int icg
,
52 int *jcg0
,int *jcg1
,ivec shift0
,ivec shift1
);
54 int dd_natoms_vsite(gmx_domdec_t
*dd
);
56 void dd_get_constraint_range(gmx_domdec_t
*dd
,
57 int *at_start
,int *at_end
);
59 real
dd_cutoff_mbody(gmx_domdec_t
*dd
);
61 real
dd_cutoff_twobody(gmx_domdec_t
*dd
);
63 gmx_bool
gmx_pmeonlynode(t_commrec
*cr
,int nodeid
);
64 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
66 void get_pme_ddnodes(t_commrec
*cr
,int pmenodeid
,
67 int *nmy_ddnodes
,int **my_ddnodes
,int *node_peer
);
68 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
70 int dd_pme_maxshift_x(gmx_domdec_t
*dd
);
71 /* Returns the maximum shift for coordinate communication in PME, dim x */
73 int dd_pme_maxshift_y(gmx_domdec_t
*dd
);
74 /* Returns the maximum shift for coordinate communication in PME, dim y */
77 void make_dd_communicators(FILE *fplog
,t_commrec
*cr
,int dd_node_order
);
81 init_domain_decomposition(FILE *fplog
,
85 real comm_distance_min
,real rconstr
,
86 const char *dlb_opt
,real dlb_scale
,
87 const char *sizex
,const char *sizey
,const char *sizez
,
88 gmx_mtop_t
*mtop
,t_inputrec
*ir
,
91 int *npme_x
, int *npme_y
);
94 void dd_init_bondeds(FILE *fplog
,
95 gmx_domdec_t
*dd
,gmx_mtop_t
*mtop
,
96 gmx_vsite_t
*vsite
,gmx_constr_t constr
,
97 t_inputrec
*ir
,gmx_bool bBCheck
,cginfo_mb_t
*cginfo_mb
);
98 /* Initialize data structures for bonded interactions */
100 gmx_bool
dd_bonded_molpbc(gmx_domdec_t
*dd
,int ePBC
);
101 /* Returns if we need to do pbc for calculating bonded interactions */
104 void set_dd_parameters(FILE *fplog
,gmx_domdec_t
*dd
,real dlb_scale
,
105 t_inputrec
*ir
,t_forcerec
*fr
,
107 /* Set DD grid dimensions and limits,
108 * should be called after calling dd_init_bondeds.
112 gmx_bool
change_dd_cutoff(t_commrec
*cr
,t_state
*state
,t_inputrec
*ir
,
114 /* Change the DD non-bonded communication cut-off.
115 * This could fail when trying to increase the cut-off,
116 * then FALSE will be returned and the cut-off is not modified.
120 void setup_dd_grid(FILE *fplog
,gmx_domdec_t
*dd
);
122 void dd_collect_vec(gmx_domdec_t
*dd
,
123 t_state
*state_local
,rvec
*lv
,rvec
*v
);
126 void dd_collect_state(gmx_domdec_t
*dd
,
127 t_state
*state_local
,t_state
*state
);
129 enum { ddCyclStep
, ddCyclPPduringPME
, ddCyclF
, ddCyclPME
, ddCyclNr
};
132 void dd_cycles_add(gmx_domdec_t
*dd
,float cycles
,int ddCycl
);
133 /* Add the wallcycle count to the DD counter */
135 void dd_force_flop_start(gmx_domdec_t
*dd
,t_nrnb
*nrnb
);
136 /* Start the force flop count */
138 void dd_force_flop_stop(gmx_domdec_t
*dd
,t_nrnb
*nrnb
);
139 /* Stop the force flop count */
142 float dd_pme_f_ratio(gmx_domdec_t
*dd
);
143 /* Return the PME/PP force load ratio, or -1 if nothing was measured.
144 * Should only be called on the DD master node.
147 void dd_move_x(gmx_domdec_t
*dd
,matrix box
,rvec x
[]);
148 /* Communicate the coordinates to the neighboring cells and do pbc. */
150 void dd_move_f(gmx_domdec_t
*dd
,rvec f
[],rvec
*fshift
);
151 /* Sum the forces over the neighboring cells.
152 * When fshift!=NULL the shift forces are updated to obtain
153 * the correct virial from the single sum including f.
156 void dd_atom_spread_real(gmx_domdec_t
*dd
,real v
[]);
157 /* Communicate a real for each atom to the neighboring cells. */
159 void dd_atom_sum_real(gmx_domdec_t
*dd
,real v
[]);
160 /* Sum the contributions to a real for each atom over the neighboring cells. */
163 void dd_partition_system(FILE *fplog
,
164 gmx_large_int_t step
,
166 gmx_bool bMasterState
,
168 t_state
*state_global
,
169 gmx_mtop_t
*top_global
,
171 t_state
*state_local
,
174 gmx_localtop_t
*top_local
,
177 gmx_shellfc_t shellfc
,
180 gmx_wallcycle_t wcycle
,
182 /* Partition the system over the nodes.
183 * step is only used for printing error messages.
184 * If bMasterState==TRUE then state_global from the master node is used,
185 * else state_local is redistributed between the nodes.
186 * When f!=NULL, *f will be reallocated to the size of state_local.
190 void reset_dd_statistics_counters(gmx_domdec_t
*dd
);
191 /* Reset all the statistics and counters for total run counting */
193 void print_dd_statistics(t_commrec
*cr
,t_inputrec
*ir
,FILE *fplog
);
195 /* In domdec_con.c */
197 void dd_move_f_vsites(gmx_domdec_t
*dd
,rvec
*f
,rvec
*fshift
);
199 void dd_clear_f_vsites(gmx_domdec_t
*dd
,rvec
*f
);
201 void dd_move_x_constraints(gmx_domdec_t
*dd
,matrix box
,
203 /* Move x0 and also x1 if x1!=NULL */
205 void dd_move_x_vsites(gmx_domdec_t
*dd
,matrix box
,rvec
*x
);
207 int *dd_constraints_nlocalatoms(gmx_domdec_t
*dd
);
209 void dd_clear_local_constraint_indices(gmx_domdec_t
*dd
);
211 void dd_clear_local_vsite_indices(gmx_domdec_t
*dd
);
213 int dd_make_local_vsites(gmx_domdec_t
*dd
,int at_start
,t_ilist
*lil
);
215 int dd_make_local_constraints(gmx_domdec_t
*dd
,int at_start
,
216 const gmx_mtop_t
*mtop
,
218 gmx_constr_t constr
,int nrec
,
221 void init_domdec_constraints(gmx_domdec_t
*dd
,
223 gmx_constr_t constr
);
225 void init_domdec_vsites(gmx_domdec_t
*dd
,int n_intercg_vsite
);
228 /* In domdec_top.c */
230 void dd_print_missing_interactions(FILE *fplog
,t_commrec
*cr
,
231 int local_count
, gmx_mtop_t
*top_global
, t_state
*state_local
);
233 void dd_make_reverse_top(FILE *fplog
,
234 gmx_domdec_t
*dd
,gmx_mtop_t
*mtop
,
235 gmx_vsite_t
*vsite
,gmx_constr_t constr
,
236 t_inputrec
*ir
,gmx_bool bBCheck
);
238 void dd_make_local_cgs(gmx_domdec_t
*dd
,t_block
*lcgs
);
240 void dd_make_local_top(FILE *fplog
,
241 gmx_domdec_t
*dd
,gmx_domdec_zones_t
*zones
,
242 int npbcdim
,matrix box
,
243 rvec cellsize_min
,ivec npulse
,
247 gmx_mtop_t
*top
,gmx_localtop_t
*ltop
);
249 void dd_sort_local_top(gmx_domdec_t
*dd
,t_mdatoms
*mdatoms
,
250 gmx_localtop_t
*ltop
);
251 /* Sort ltop->ilist when we are doing free energy. */
254 gmx_localtop_t
*dd_init_local_top(gmx_mtop_t
*top_global
);
257 void dd_init_local_state(gmx_domdec_t
*dd
,
258 t_state
*state_global
,t_state
*local_state
);
260 t_blocka
*make_charge_group_links(gmx_mtop_t
*mtop
,gmx_domdec_t
*dd
,
261 cginfo_mb_t
*cginfo_mb
);
263 void dd_bonded_cg_distance(FILE *fplog
,
264 gmx_domdec_t
*dd
,gmx_mtop_t
*mtop
,
265 t_inputrec
*ir
,rvec
*x
,matrix box
,
267 real
*r_2b
,real
*r_mb
);
269 void write_dd_pdb(const char *fn
,gmx_large_int_t step
,const char *title
,
272 int natoms
,rvec x
[],matrix box
);
273 /* Dump a pdb file with the current DD home + communicated atoms.
274 * When natoms=-1, dump all known atoms.
278 /* In domdec_setup.c */
280 real
comm_box_frac(ivec dd_nc
,real cutoff
,gmx_ddbox_t
*ddbox
);
281 /* Returns the volume fraction of the system that is communicated */
283 real
dd_choose_grid(FILE *fplog
,
284 t_commrec
*cr
,gmx_domdec_t
*dd
,t_inputrec
*ir
,
285 gmx_mtop_t
*mtop
,matrix box
,gmx_ddbox_t
*ddbox
,
286 gmx_bool bDynLoadBal
,real dlb_scale
,
287 real cellsize_limit
,real cutoff_dd
,
288 gmx_bool bInterCGBondeds
,gmx_bool bInterCGMultiBody
);
289 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
291 * On the master node returns the actual cellsize limit used.
295 /* In domdec_box.c */
297 void set_ddbox(gmx_domdec_t
*dd
,gmx_bool bMasterState
,t_commrec
*cr_sum
,
298 t_inputrec
*ir
,matrix box
,
299 gmx_bool bCalcUnboundedSize
,t_block
*cgs
,rvec
*x
,
302 void set_ddbox_cr(t_commrec
*cr
,ivec
*dd_nc
,
303 t_inputrec
*ir
,matrix box
,t_block
*cgs
,rvec
*x
,
310 #endif /* _domdec_h */