-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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-
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+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/vsite.h"
#include <stdio.h>
-#include "typedefs.h"
-#include "vsite.h"
-#include "macros.h"
-#include "smalloc.h"
-#include "nrnb.h"
-#include "vec.h"
-#include "mvdata.h"
-#include "network.h"
-#include "mshift.h"
-#include "pbc.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
-#include "gmx_omp.h"
+
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
/* Routines to send/recieve coordinates and force
* of constructing atoms.
*/
-static void move_construct_x(t_comm_vsites *vsitecomm, rvec x[], t_commrec *cr)
-{
- rvec *sendbuf;
- rvec *recvbuf;
- int i, ia;
-
- sendbuf = vsitecomm->send_buf;
- recvbuf = vsitecomm->recv_buf;
-
-
- /* Prepare pulse left by copying to send buffer */
- for (i = 0; i < vsitecomm->left_export_nconstruct; i++)
- {
- ia = vsitecomm->left_export_construct[i];
- copy_rvec(x[ia], sendbuf[i]);
- }
-
- /* Pulse coordinates left */
- gmx_tx_rx_real(cr, GMX_LEFT, (real *)sendbuf, 3*vsitecomm->left_export_nconstruct, GMX_RIGHT, (real *)recvbuf, 3*vsitecomm->right_import_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for (i = 0; i < vsitecomm->right_import_nconstruct; i++)
- {
- ia = vsitecomm->right_import_construct[i];
- copy_rvec(recvbuf[i], x[ia]);
- }
-
- /* Prepare pulse right by copying to send buffer */
- for (i = 0; i < vsitecomm->right_export_nconstruct; i++)
- {
- ia = vsitecomm->right_export_construct[i];
- copy_rvec(x[ia], sendbuf[i]);
- }
-
- /* Pulse coordinates right */
- gmx_tx_rx_real(cr, GMX_RIGHT, (real *)sendbuf, 3*vsitecomm->right_export_nconstruct, GMX_LEFT, (real *)recvbuf, 3*vsitecomm->left_import_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for (i = 0; i < vsitecomm->left_import_nconstruct; i++)
- {
- ia = vsitecomm->left_import_construct[i];
- copy_rvec(recvbuf[i], x[ia]);
- }
-}
-
-
-static void move_construct_f(t_comm_vsites *vsitecomm, rvec f[], t_commrec *cr)
-{
- rvec *sendbuf;
- rvec *recvbuf;
- int i, ia;
-
- sendbuf = vsitecomm->send_buf;
- recvbuf = vsitecomm->recv_buf;
-
- /* Prepare pulse right by copying to send buffer */
- for (i = 0; i < vsitecomm->right_import_nconstruct; i++)
- {
- ia = vsitecomm->right_import_construct[i];
- copy_rvec(f[ia], sendbuf[i]);
- clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
- }
-
- /* Pulse forces right */
- gmx_tx_rx_real(cr, GMX_RIGHT, (real *)sendbuf, 3*vsitecomm->right_import_nconstruct, GMX_LEFT, (real *)recvbuf, 3*vsitecomm->left_export_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for (i = 0; i < vsitecomm->left_export_nconstruct; i++)
- {
- ia = vsitecomm->left_export_construct[i];
- rvec_inc(f[ia], recvbuf[i]);
- }
-
- /* Prepare pulse left by copying to send buffer */
- for (i = 0; i < vsitecomm->left_import_nconstruct; i++)
- {
- ia = vsitecomm->left_import_construct[i];
- copy_rvec(f[ia], sendbuf[i]);
- clear_rvec(f[ia]); /* Zero it here after moving, just to simplify debug book-keeping... */
- }
-
- /* Pulse coordinates left */
- gmx_tx_rx_real(cr, GMX_LEFT, (real *)sendbuf, 3*vsitecomm->left_import_nconstruct, GMX_RIGHT, (real *)recvbuf, 3*vsitecomm->right_export_nconstruct);
-
- /* Copy from receive buffer to coordinate array */
- for (i = 0; i < vsitecomm->right_export_nconstruct; i++)
- {
- ia = vsitecomm->right_export_construct[i];
- rvec_inc(f[ia], recvbuf[i]);
- }
-
- /* All forces are now on the home processors */
-}
-
-
-static void
-pd_clear_nonlocal_constructs(t_comm_vsites *vsitecomm, rvec f[])
-{
- int i, ia;
-
- for (i = 0; i < vsitecomm->left_import_nconstruct; i++)
- {
- ia = vsitecomm->left_import_construct[i];
- clear_rvec(f[ia]);
- }
- for (i = 0; i < vsitecomm->right_import_nconstruct; i++)
- {
- ia = vsitecomm->right_import_construct[i];
- clear_rvec(f[ia]);
- }
-}
-
-
-
static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
{
if (pbc)
void construct_vsites_thread(gmx_vsite_t *vsite,
- rvec x[], t_nrnb *nrnb,
+ rvec x[],
real dt, rvec *v,
t_iparams ip[], t_ilist ilist[],
t_pbc *pbc_null)
}
}
-void construct_vsites(FILE *log, gmx_vsite_t *vsite,
- rvec x[], t_nrnb *nrnb,
+void construct_vsites(gmx_vsite_t *vsite,
+ rvec x[],
real dt, rvec *v,
t_iparams ip[], t_ilist ilist[],
- int ePBC, gmx_bool bMolPBC, t_graph *graph,
+ int ePBC, gmx_bool bMolPBC,
t_commrec *cr, matrix box)
{
t_pbc pbc, *pbc_null;
pbc_null = NULL;
}
- if (cr)
+ if (bDomDec)
{
- if (bDomDec)
- {
- dd_move_x_vsites(cr->dd, box, x);
- }
- else if (vsite->bPDvsitecomm)
- {
- /* I'm not sure whether the periodicity and shift are guaranteed
- * to be consistent between different nodes when running e.g. polymers
- * in parallel. In this special case we thus unshift/shift,
- * but only when necessary. This is to make sure the coordinates
- * we move don't end up a box away...
- */
- if (graph != NULL)
- {
- unshift_self(graph, box, x);
- }
-
- move_construct_x(vsite->vsitecomm, x, cr);
-
- if (graph != NULL)
- {
- shift_self(graph, box, x);
- }
- }
+ dd_move_x_vsites(cr->dd, box, x);
}
if (vsite->nthreads == 1)
{
construct_vsites_thread(vsite,
- x, nrnb, dt, v,
+ x, dt, v,
ip, ilist,
pbc_null);
}
#pragma omp parallel num_threads(vsite->nthreads)
{
construct_vsites_thread(vsite,
- x, nrnb, dt, v,
+ x, dt, v,
ip, vsite->tdata[gmx_omp_get_thread_num()].ilist,
pbc_null);
}
/* Now we can construct the vsites that might depend on other vsites */
construct_vsites_thread(vsite,
- x, nrnb, dt, v,
+ x, dt, v,
ip, vsite->tdata[vsite->nthreads].ilist,
pbc_null);
}
/* TOTAL: 13 flops */
}
-void construct_vsites_mtop(FILE *log, gmx_vsite_t *vsite,
+void construct_vsites_mtop(gmx_vsite_t *vsite,
gmx_mtop_t *mtop, rvec x[])
{
int as, mb, mol;
molt = &mtop->moltype[molb->type];
for (mol = 0; mol < molb->nmol; mol++)
{
- construct_vsites(log, vsite, x+as, NULL, 0.0, NULL,
+ construct_vsites(vsite, x+as, 0.0, NULL,
mtop->ffparams.iparams, molt->ilist,
- epbcNONE, TRUE, NULL, NULL, NULL);
+ epbcNONE, TRUE, NULL, NULL);
as += molt->atoms.nr;
}
}
}
}
-void spread_vsite_f(FILE *log, gmx_vsite_t *vsite,
+void spread_vsite_f(gmx_vsite_t *vsite,
rvec x[], rvec f[], rvec *fshift,
gmx_bool VirCorr, matrix vir,
t_nrnb *nrnb, t_idef *idef,
{
dd_clear_f_vsites(cr->dd, f);
}
- else if (PARTDECOMP(cr) && vsite->vsitecomm != NULL)
- {
- pd_clear_nonlocal_constructs(vsite->vsitecomm, f);
- }
if (vsite->nthreads == 1)
{
{
dd_move_f_vsites(cr->dd, f, fshift);
}
- else if (vsite->bPDvsitecomm)
- {
- /* We only move forces here, and they are independent of shifts */
- move_construct_f(vsite->vsitecomm, f, cr);
- }
inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
}
void split_vsites_over_threads(const t_ilist *ilist,
+ const t_iparams *ip,
const t_mdatoms *mdatoms,
gmx_bool bLimitRange,
gmx_vsite_t *vsite)
vsite_atom_range = -1;
for (ftype = 0; ftype < F_NRE; ftype++)
{
- if ((interaction_function[ftype].flags & IF_VSITE) &&
- ftype != F_VSITEN)
+ if (interaction_function[ftype].flags & IF_VSITE)
{
- nral1 = 1 + NRAL(ftype);
- iat = ilist[ftype].iatoms;
- for (i = 0; i < ilist[ftype].nr; i += nral1)
+ if (ftype != F_VSITEN)
{
- for (j = i+1; j < i+nral1; j++)
+ nral1 = 1 + NRAL(ftype);
+ iat = ilist[ftype].iatoms;
+ for (i = 0; i < ilist[ftype].nr; i += nral1)
{
- vsite_atom_range = max(vsite_atom_range, iat[j]);
+ for (j = i + 1; j < i + nral1; j++)
+ {
+ vsite_atom_range = max(vsite_atom_range, iat[j]);
+ }
+ }
+ }
+ else
+ {
+ int vs_ind_end;
+
+ iat = ilist[ftype].iatoms;
+
+ i = 0;
+ while (i < ilist[ftype].nr)
+ {
+ /* The 3 below is from 1+NRAL(ftype)=3 */
+ vs_ind_end = i + ip[iat[i]].vsiten.n*3;
+
+ vsite_atom_range = max(vsite_atom_range, iat[i+1]);
+ while (i < vs_ind_end)
+ {
+ vsite_atom_range = max(vsite_atom_range, iat[i+2]);
+ i += 3;
+ }
}
}
}
for (ftype = 0; ftype < F_NRE; ftype++)
{
- if ((interaction_function[ftype].flags & IF_VSITE) &&
- ftype != F_VSITEN)
+ if (interaction_function[ftype].flags & IF_VSITE)
{
nral1 = 1 + NRAL(ftype);
inc = nral1;
*/
if (ftype != F_VSITEN)
{
- for (j = i+2; j < i+nral1; j++)
+ for (j = i + 2; j < i + nral1; j++)
{
if (th_ind[iat[j]] != th)
{
}
else
{
- inc = iat[i];
- for (j = i+2; j < i+inc; j += 3)
+ /* The 3 below is from 1+NRAL(ftype)=3 */
+ inc = ip[iat[i]].vsiten.n*3;
+ for (j = i + 2; j < i + inc; j += 3)
{
if (th_ind[iat[j]] != th)
{
}
/* Copy this vsite to the thread data struct of thread th */
il_th = &vsite->tdata[th].ilist[ftype];
- for (j = i; j < i+inc; j++)
+ for (j = i; j < i + inc; j++)
{
il_th->iatoms[il_th->nr++] = iat[j];
}
sfree(a2cg);
}
- if (PARTDECOMP(cr))
- {
- snew(vsite->vsitecomm, 1);
- vsite->bPDvsitecomm =
- setup_parallel_vsites(&(top->idef), cr, vsite->vsitecomm);
- }
}
if (vsite->nthreads > 1)
{
- if (vsite->bHaveChargeGroups || PARTDECOMP(cr))
+ if (vsite->bHaveChargeGroups)
{
- gmx_incons("Can not use threads virtual sites combined with charge groups or particle decomposition");
+ gmx_fatal(FARGS, "The combination of threading, virtual sites and charge groups is not implemented");
}
- split_vsites_over_threads(top->idef.il, md, !DOMAINDECOMP(cr), vsite);
+ split_vsites_over_threads(top->idef.il, top->idef.iparams,
+ md, !DOMAINDECOMP(cr), vsite);
}
}
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