* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief This file implements functions for domdec to use
+ * while managing inter-atomic constraints.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
#include "gmxpre.h"
+#include "domdec_constraints.h"
+
#include <assert.h>
#include <algorithm>
#include "gromacs/domdec/domdec.h"
-#include "gromacs/domdec/domdec_network.h"
#include "gromacs/legacyheaders/constr.h"
#include "gromacs/legacyheaders/gmx_ga2la.h"
#include "gromacs/legacyheaders/gmx_hash.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-typedef struct {
- int nsend;
- int *a;
- int a_nalloc;
- int nrecv;
-} gmx_specatsend_t;
-
-typedef struct {
- int *ind;
- int nalloc;
- int n;
-} ind_req_t;
-
-typedef struct gmx_domdec_specat_comm {
- /* The number of indices to receive during the setup */
- int nreq[DIM][2][2];
- /* The atoms to send */
- gmx_specatsend_t spas[DIM][2];
- gmx_bool *bSendAtom;
- int bSendAtom_nalloc;
- /* Send buffers */
- int *ibuf;
- int ibuf_nalloc;
- rvec *vbuf;
- int vbuf_nalloc;
- rvec *vbuf2;
- int vbuf2_nalloc;
- /* The range in the local buffer(s) for received atoms */
- int at_start;
- int at_end;
-
- /* The atom indices we need from the surrounding cells.
- * We can gather the indices over nthread threads.
- */
- int nthread;
- ind_req_t *ireq;
-} gmx_domdec_specat_comm_t;
+#include "domdec_specatomcomm.h"
+/*! \brief Struct used during constraint setup with domain decomposition */
typedef struct gmx_domdec_constraints {
- int *molb_con_offset;
- int *molb_ncon_mol;
- /* The fully local and connected constraints */
- int ncon;
+ //! @cond Doxygen_Suppress
+ int *molb_con_offset; /**< Offset in the constraint array for each molblock */
+ int *molb_ncon_mol; /**< The number of constraints per molecule for each molblock */
+
+ int ncon; /**< The fully local and conneced constraints */
/* The global constraint number, only required for clearing gc_req */
- int *con_gl;
- int *con_nlocat;
- int con_nalloc;
- /* Boolean that tells if a global constraint index has been requested */
- char *gc_req;
- /* Global to local communicated constraint atom only index */
- gmx_hash_t ga2la;
+ int *con_gl; /**< Global constraint indices for local constraints */
+ int *con_nlocat; /**< Number of local atoms (2/1/0) for each constraint */
+ int con_nalloc; /**< Allocation size for \p con_gl and \p con_nlocat */
+
+ char *gc_req; /**< Boolean that tells if a global constraint index has been requested; note: size global #constraints */
+ gmx_hash_t ga2la; /**< Global to local communicated constraint atom only index */
/* Multi-threading stuff */
- int nthread;
- t_ilist *ils;
+ int nthread; /**< Number of threads used for DD constraint setup */
+ t_ilist *ils; /**< Constraint ilist working arrays, size \p nthread */
+ //! @endcond
} gmx_domdec_constraints_t;
-
-static void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
- rvec *f, rvec *fshift)
-{
- gmx_specatsend_t *spas;
- rvec *vbuf;
- int n, n0, n1, d, dim, dir, i;
- ivec vis;
- int is;
- gmx_bool bPBC, bScrew;
-
- n = spac->at_end;
- for (d = dd->ndim-1; d >= 0; d--)
- {
- dim = dd->dim[d];
- if (dd->nc[dim] > 2)
- {
- /* Pulse the grid forward and backward */
- spas = spac->spas[d];
- n0 = spas[0].nrecv;
- n1 = spas[1].nrecv;
- n -= n1 + n0;
- vbuf = spac->vbuf;
- /* Send and receive the coordinates */
- dd_sendrecv2_rvec(dd, d,
- f+n+n1, n0, vbuf, spas[0].nsend,
- f+n, n1, vbuf+spas[0].nsend, spas[1].nsend);
- for (dir = 0; dir < 2; dir++)
- {
- bPBC = ((dir == 0 && dd->ci[dim] == 0) ||
- (dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
- bScrew = (bPBC && dd->bScrewPBC && dim == XX);
-
- spas = &spac->spas[d][dir];
- /* Sum the buffer into the required forces */
- if (!bPBC || (!bScrew && fshift == NULL))
- {
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_inc(f[spas->a[i]], *vbuf);
- vbuf++;
- }
- }
- else
- {
- clear_ivec(vis);
- vis[dim] = (dir == 0 ? 1 : -1);
- is = IVEC2IS(vis);
- if (!bScrew)
- {
- /* Sum and add to shift forces */
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_inc(f[spas->a[i]], *vbuf);
- rvec_inc(fshift[is], *vbuf);
- vbuf++;
- }
- }
- else
- {
- /* Rotate the forces */
- for (i = 0; i < spas->nsend; i++)
- {
- f[spas->a[i]][XX] += (*vbuf)[XX];
- f[spas->a[i]][YY] -= (*vbuf)[YY];
- f[spas->a[i]][ZZ] -= (*vbuf)[ZZ];
- if (fshift)
- {
- rvec_inc(fshift[is], *vbuf);
- }
- vbuf++;
- }
- }
- }
- }
- }
- else
- {
- /* Two cells, so we only need to communicate one way */
- spas = &spac->spas[d][0];
- n -= spas->nrecv;
- /* Send and receive the coordinates */
- dd_sendrecv_rvec(dd, d, dddirForward,
- f+n, spas->nrecv, spac->vbuf, spas->nsend);
- /* Sum the buffer into the required forces */
- if (dd->bScrewPBC && dim == XX &&
- (dd->ci[dim] == 0 ||
- dd->ci[dim] == dd->nc[dim]-1))
- {
- for (i = 0; i < spas->nsend; i++)
- {
- /* Rotate the force */
- f[spas->a[i]][XX] += spac->vbuf[i][XX];
- f[spas->a[i]][YY] -= spac->vbuf[i][YY];
- f[spas->a[i]][ZZ] -= spac->vbuf[i][ZZ];
- }
- }
- else
- {
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_inc(f[spas->a[i]], spac->vbuf[i]);
- }
- }
- }
- }
-}
-
-void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift)
-{
- if (dd->vsite_comm)
- {
- dd_move_f_specat(dd, dd->vsite_comm, f, fshift);
- }
-}
-
-void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f)
-{
- int i;
-
- if (dd->vsite_comm)
- {
- for (i = dd->vsite_comm->at_start; i < dd->vsite_comm->at_end; i++)
- {
- clear_rvec(f[i]);
- }
- }
-}
-
-static void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
- matrix box,
- rvec *x0,
- rvec *x1, gmx_bool bX1IsCoord)
-{
- gmx_specatsend_t *spas;
- rvec *x, *vbuf, *rbuf;
- int nvec, v, n, nn, ns0, ns1, nr0, nr1, nr, d, dim, dir, i;
- gmx_bool bPBC, bScrew = FALSE;
- rvec shift = {0, 0, 0};
-
- nvec = 1;
- if (x1 != NULL)
- {
- nvec++;
- }
-
- n = spac->at_start;
- for (d = 0; d < dd->ndim; d++)
- {
- dim = dd->dim[d];
- if (dd->nc[dim] > 2)
- {
- /* Pulse the grid forward and backward */
- vbuf = spac->vbuf;
- for (dir = 0; dir < 2; dir++)
- {
- if (dir == 0 && dd->ci[dim] == 0)
- {
- bPBC = TRUE;
- bScrew = (dd->bScrewPBC && dim == XX);
- copy_rvec(box[dim], shift);
- }
- else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
- {
- bPBC = TRUE;
- bScrew = (dd->bScrewPBC && dim == XX);
- for (i = 0; i < DIM; i++)
- {
- shift[i] = -box[dim][i];
- }
- }
- else
- {
- bPBC = FALSE;
- bScrew = FALSE;
- }
- spas = &spac->spas[d][dir];
- for (v = 0; v < nvec; v++)
- {
- x = (v == 0 ? x0 : x1);
- /* Copy the required coordinates to the send buffer */
- if (!bPBC || (v == 1 && !bX1IsCoord))
- {
- /* Only copy */
- for (i = 0; i < spas->nsend; i++)
- {
- copy_rvec(x[spas->a[i]], *vbuf);
- vbuf++;
- }
- }
- else if (!bScrew)
- {
- /* Shift coordinates */
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_add(x[spas->a[i]], shift, *vbuf);
- vbuf++;
- }
- }
- else
- {
- /* Shift and rotate coordinates */
- for (i = 0; i < spas->nsend; i++)
- {
- (*vbuf)[XX] = x[spas->a[i]][XX] + shift[XX];
- (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY] + shift[YY];
- (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ] + shift[ZZ];
- vbuf++;
- }
- }
- }
- }
- /* Send and receive the coordinates */
- spas = spac->spas[d];
- ns0 = spas[0].nsend;
- nr0 = spas[0].nrecv;
- ns1 = spas[1].nsend;
- nr1 = spas[1].nrecv;
- if (nvec == 1)
- {
- dd_sendrecv2_rvec(dd, d,
- spac->vbuf+ns0, ns1, x0+n, nr1,
- spac->vbuf, ns0, x0+n+nr1, nr0);
- }
- else
- {
- /* Communicate both vectors in one buffer */
- rbuf = spac->vbuf2;
- dd_sendrecv2_rvec(dd, d,
- spac->vbuf+2*ns0, 2*ns1, rbuf, 2*nr1,
- spac->vbuf, 2*ns0, rbuf+2*nr1, 2*nr0);
- /* Split the buffer into the two vectors */
- nn = n;
- for (dir = 1; dir >= 0; dir--)
- {
- nr = spas[dir].nrecv;
- for (v = 0; v < 2; v++)
- {
- x = (v == 0 ? x0 : x1);
- for (i = 0; i < nr; i++)
- {
- copy_rvec(*rbuf, x[nn+i]);
- rbuf++;
- }
- }
- nn += nr;
- }
- }
- n += nr0 + nr1;
- }
- else
- {
- spas = &spac->spas[d][0];
- /* Copy the required coordinates to the send buffer */
- vbuf = spac->vbuf;
- for (v = 0; v < nvec; v++)
- {
- x = (v == 0 ? x0 : x1);
- if (dd->bScrewPBC && dim == XX &&
- (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
- {
- /* Here we only perform the rotation, the rest of the pbc
- * is handled in the constraint or viste routines.
- */
- for (i = 0; i < spas->nsend; i++)
- {
- (*vbuf)[XX] = x[spas->a[i]][XX];
- (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY];
- (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ];
- vbuf++;
- }
- }
- else
- {
- for (i = 0; i < spas->nsend; i++)
- {
- copy_rvec(x[spas->a[i]], *vbuf);
- vbuf++;
- }
- }
- }
- /* Send and receive the coordinates */
- if (nvec == 1)
- {
- dd_sendrecv_rvec(dd, d, dddirBackward,
- spac->vbuf, spas->nsend, x0+n, spas->nrecv);
- }
- else
- {
- /* Communicate both vectors in one buffer */
- rbuf = spac->vbuf2;
- dd_sendrecv_rvec(dd, d, dddirBackward,
- spac->vbuf, 2*spas->nsend, rbuf, 2*spas->nrecv);
- /* Split the buffer into the two vectors */
- nr = spas[0].nrecv;
- for (v = 0; v < 2; v++)
- {
- x = (v == 0 ? x0 : x1);
- for (i = 0; i < nr; i++)
- {
- copy_rvec(*rbuf, x[n+i]);
- rbuf++;
- }
- }
- }
- n += spas->nrecv;
- }
- }
-}
-
void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
rvec *x0, rvec *x1, gmx_bool bX1IsCoord)
{
}
}
-void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x)
-{
- if (dd->vsite_comm)
- {
- dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
- }
-}
-
int *dd_constraints_nlocalatoms(gmx_domdec_t *dd)
{
if (dd->constraints)
}
}
-static int setup_specat_communication(gmx_domdec_t *dd,
- ind_req_t *ireq,
- gmx_domdec_specat_comm_t *spac,
- gmx_hash_t ga2la_specat,
- int at_start,
- int vbuf_fac,
- const char *specat_type,
- const char *add_err)
-{
- int nsend[2], nlast, nsend_zero[2] = {0, 0}, *nsend_ptr;
- int d, dim, ndir, dir, nr, ns, i, nrecv_local, n0, start, indr, ind, buf[2];
- int nat_tot_specat, nat_tot_prev, nalloc_old;
- gmx_bool bPBC;
- gmx_specatsend_t *spas;
-
- if (debug)
- {
- fprintf(debug, "Begin setup_specat_communication for %s\n", specat_type);
- }
-
- /* nsend[0]: the number of atoms requested by this node only,
- * we communicate this for more efficients checks
- * nsend[1]: the total number of requested atoms
- */
- nsend[0] = ireq->n;
- nsend[1] = nsend[0];
- nlast = nsend[1];
- for (d = dd->ndim-1; d >= 0; d--)
- {
- /* Pulse the grid forward and backward */
- dim = dd->dim[d];
- bPBC = (dim < dd->npbcdim);
- if (dd->nc[dim] == 2)
- {
- /* Only 2 cells, so we only need to communicate once */
- ndir = 1;
- }
- else
- {
- ndir = 2;
- }
- for (dir = 0; dir < ndir; dir++)
- {
- if (!bPBC &&
- dd->nc[dim] > 2 &&
- ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) ||
- (dir == 1 && dd->ci[dim] == 0)))
- {
- /* No pbc: the fist/last cell should not request atoms */
- nsend_ptr = nsend_zero;
- }
- else
- {
- nsend_ptr = nsend;
- }
- /* Communicate the number of indices */
- dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
- nsend_ptr, 2, spac->nreq[d][dir], 2);
- nr = spac->nreq[d][dir][1];
- if (nlast+nr > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_dd(nlast+nr);
- srenew(ireq->ind, ireq->nalloc);
- }
- /* Communicate the indices */
- dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
- ireq->ind, nsend_ptr[1], ireq->ind+nlast, nr);
- nlast += nr;
- }
- nsend[1] = nlast;
- }
- if (debug)
- {
- fprintf(debug, "Communicated the counts\n");
- }
-
- /* Search for the requested atoms and communicate the indices we have */
- nat_tot_specat = at_start;
- nrecv_local = 0;
- for (d = 0; d < dd->ndim; d++)
- {
- /* Pulse the grid forward and backward */
- if (dd->dim[d] >= dd->npbcdim || dd->nc[dd->dim[d]] > 2)
- {
- ndir = 2;
- }
- else
- {
- ndir = 1;
- }
- nat_tot_prev = nat_tot_specat;
- for (dir = ndir-1; dir >= 0; dir--)
- {
- if (nat_tot_specat > spac->bSendAtom_nalloc)
- {
- nalloc_old = spac->bSendAtom_nalloc;
- spac->bSendAtom_nalloc = over_alloc_dd(nat_tot_specat);
- srenew(spac->bSendAtom, spac->bSendAtom_nalloc);
- for (i = nalloc_old; i < spac->bSendAtom_nalloc; i++)
- {
- spac->bSendAtom[i] = FALSE;
- }
- }
- spas = &spac->spas[d][dir];
- n0 = spac->nreq[d][dir][0];
- nr = spac->nreq[d][dir][1];
- if (debug)
- {
- fprintf(debug, "dim=%d, dir=%d, searching for %d atoms\n",
- d, dir, nr);
- }
- start = nlast - nr;
- spas->nsend = 0;
- nsend[0] = 0;
- for (i = 0; i < nr; i++)
- {
- indr = ireq->ind[start+i];
- ind = -1;
- /* Check if this is a home atom and if so ind will be set */
- if (!ga2la_get_home(dd->ga2la, indr, &ind))
- {
- /* Search in the communicated atoms */
- ind = gmx_hash_get_minone(ga2la_specat, indr);
- }
- if (ind >= 0)
- {
- if (i < n0 || !spac->bSendAtom[ind])
- {
- if (spas->nsend+1 > spas->a_nalloc)
- {
- spas->a_nalloc = over_alloc_large(spas->nsend+1);
- srenew(spas->a, spas->a_nalloc);
- }
- /* Store the local index so we know which coordinates
- * to send out later.
- */
- spas->a[spas->nsend] = ind;
- spac->bSendAtom[ind] = TRUE;
- if (spas->nsend+1 > spac->ibuf_nalloc)
- {
- spac->ibuf_nalloc = over_alloc_large(spas->nsend+1);
- srenew(spac->ibuf, spac->ibuf_nalloc);
- }
- /* Store the global index so we can send it now */
- spac->ibuf[spas->nsend] = indr;
- if (i < n0)
- {
- nsend[0]++;
- }
- spas->nsend++;
- }
- }
- }
- nlast = start;
- /* Clear the local flags */
- for (i = 0; i < spas->nsend; i++)
- {
- spac->bSendAtom[spas->a[i]] = FALSE;
- }
- /* Send and receive the number of indices to communicate */
- nsend[1] = spas->nsend;
- dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
- nsend, 2, buf, 2);
- if (debug)
- {
- fprintf(debug, "Send to rank %d, %d (%d) indices, "
- "receive from rank %d, %d (%d) indices\n",
- dd->neighbor[d][1-dir], nsend[1], nsend[0],
- dd->neighbor[d][dir], buf[1], buf[0]);
- if (gmx_debug_at)
- {
- for (i = 0; i < spas->nsend; i++)
- {
- fprintf(debug, " %d", spac->ibuf[i]+1);
- }
- fprintf(debug, "\n");
- }
- }
- nrecv_local += buf[0];
- spas->nrecv = buf[1];
- if (nat_tot_specat + spas->nrecv > dd->gatindex_nalloc)
- {
- dd->gatindex_nalloc =
- over_alloc_dd(nat_tot_specat + spas->nrecv);
- srenew(dd->gatindex, dd->gatindex_nalloc);
- }
- /* Send and receive the indices */
- dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
- spac->ibuf, spas->nsend,
- dd->gatindex+nat_tot_specat, spas->nrecv);
- nat_tot_specat += spas->nrecv;
- }
-
- /* Allocate the x/f communication buffers */
- ns = spac->spas[d][0].nsend;
- nr = spac->spas[d][0].nrecv;
- if (ndir == 2)
- {
- ns += spac->spas[d][1].nsend;
- nr += spac->spas[d][1].nrecv;
- }
- if (vbuf_fac*ns > spac->vbuf_nalloc)
- {
- spac->vbuf_nalloc = over_alloc_dd(vbuf_fac*ns);
- srenew(spac->vbuf, spac->vbuf_nalloc);
- }
- if (vbuf_fac == 2 && vbuf_fac*nr > spac->vbuf2_nalloc)
- {
- spac->vbuf2_nalloc = over_alloc_dd(vbuf_fac*nr);
- srenew(spac->vbuf2, spac->vbuf2_nalloc);
- }
-
- /* Make a global to local index for the communication atoms */
- for (i = nat_tot_prev; i < nat_tot_specat; i++)
- {
- gmx_hash_change_or_set(ga2la_specat, dd->gatindex[i], i);
- }
- }
-
- /* Check that in the end we got the number of atoms we asked for */
- if (nrecv_local != ireq->n)
- {
- if (debug)
- {
- fprintf(debug, "Requested %d, received %d (tot recv %d)\n",
- ireq->n, nrecv_local, nat_tot_specat-at_start);
- if (gmx_debug_at)
- {
- for (i = 0; i < ireq->n; i++)
- {
- ind = gmx_hash_get_minone(ga2la_specat, ireq->ind[i]);
- fprintf(debug, " %s%d",
- (ind >= 0) ? "" : "!",
- ireq->ind[i]+1);
- }
- fprintf(debug, "\n");
- }
- }
- fprintf(stderr, "\nDD cell %d %d %d: Neighboring cells do not have atoms:",
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
- for (i = 0; i < ireq->n; i++)
- {
- if (gmx_hash_get_minone(ga2la_specat, ireq->ind[i]) < 0)
- {
- fprintf(stderr, " %d", ireq->ind[i]+1);
- }
- }
- fprintf(stderr, "\n");
- gmx_fatal(FARGS, "DD cell %d %d %d could only obtain %d of the %d atoms that are connected via %ss from the neighboring cells. This probably means your %s lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells%s%s.",
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ],
- nrecv_local, ireq->n, specat_type,
- specat_type, add_err,
- dd->bGridJump ? " or use the -rcon option of mdrun" : "");
- }
-
- spac->at_start = at_start;
- spac->at_end = nat_tot_specat;
-
- if (debug)
- {
- fprintf(debug, "Done setup_specat_communication\n");
- }
-
- return nat_tot_specat;
-}
-
+/*! \brief Walks over the constraints out from the local atoms into the non-local atoms and adds them to a list */
static void walk_out(int con, int con_offset, int a, int offset, int nrec,
int ncon1, const t_iatom *ia1, const t_iatom *ia2,
const t_blocka *at2con,
}
}
+/*! \brief Looks up SETTLE constraints for a range of charge-groups */
static void atoms_to_settles(gmx_domdec_t *dd,
const gmx_mtop_t *mtop,
const int *cginfo,
gmx_mtop_atomlookup_destroy(alook);
}
+/*! \brief Looks up constraint for the local atoms */
static void atoms_to_constraints(gmx_domdec_t *dd,
const gmx_mtop_t *mtop,
const int *cginfo,
return at_end;
}
-int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
-{
- gmx_domdec_specat_comm_t *spac;
- ind_req_t *ireq;
- gmx_hash_t ga2la_specat;
- int ftype, nral, i, j, a;
- t_ilist *lilf;
- t_iatom *iatoms;
- int at_end;
-
- spac = dd->vsite_comm;
- ireq = &spac->ireq[0];
- ga2la_specat = dd->ga2la_vsite;
-
- ireq->n = 0;
- /* Loop over all the home vsites */
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (interaction_function[ftype].flags & IF_VSITE)
- {
- nral = NRAL(ftype);
- lilf = &lil[ftype];
- for (i = 0; i < lilf->nr; i += 1+nral)
- {
- iatoms = lilf->iatoms + i;
- /* Check if we have the other atoms */
- for (j = 1; j < 1+nral; j++)
- {
- if (iatoms[j] < 0)
- {
- /* This is not a home atom,
- * we need to ask our neighbors.
- */
- a = -iatoms[j] - 1;
- /* Check to not ask for the same atom more than once */
- if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
- {
- /* Add this non-home atom to the list */
- if (ireq->n+1 > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_large(ireq->n+1);
- srenew(ireq->ind, ireq->nalloc);
- }
- ireq->ind[ireq->n++] = a;
- /* Temporarily mark with -2,
- * we get the index later.
- */
- gmx_hash_set(ga2la_specat, a, -2);
- }
- }
- }
- }
- }
- }
-
- at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
- at_start, 1, "vsite", "");
-
- /* Fill in the missing indices */
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (interaction_function[ftype].flags & IF_VSITE)
- {
- nral = NRAL(ftype);
- lilf = &lil[ftype];
- for (i = 0; i < lilf->nr; i += 1+nral)
- {
- iatoms = lilf->iatoms + i;
- for (j = 1; j < 1+nral; j++)
- {
- if (iatoms[j] < 0)
- {
- iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
- }
- }
- }
- }
- }
-
- return at_end;
-}
-
-static gmx_domdec_specat_comm_t *specat_comm_init(int nthread)
-{
- gmx_domdec_specat_comm_t *spac;
-
- snew(spac, 1);
- spac->nthread = nthread;
- snew(spac->ireq, spac->nthread);
-
- return spac;
-}
-
void init_domdec_constraints(gmx_domdec_t *dd,
gmx_mtop_t *mtop)
{
dd->constraint_comm = specat_comm_init(dc->nthread);
}
-
-void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
-{
- if (debug)
- {
- fprintf(debug, "Begin init_domdec_vsites\n");
- }
-
- /* Use a hash table for the global to local index.
- * The number of keys is a rough estimate, it will be optimized later.
- */
- dd->ga2la_vsite = gmx_hash_init(std::min(n_intercg_vsite/20,
- n_intercg_vsite/(2*dd->nnodes)));
-
- dd->vsite_comm = specat_comm_init(1);
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff