/*
+ * 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.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * 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,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
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- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
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*
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*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * GRoups of Organic Molecules in ACtion for Science
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _commrec_h
#define _commrec_h
-#include "../../utility/gmxmpi.h"
-#include "idef.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/gmxmpi.h"
#ifdef __cplusplus
extern "C" {
rvec bb_x1; /* Zone bounding box upper corner in Cartesian coords */
} gmx_domdec_zone_size_t;
-typedef struct {
+struct gmx_domdec_zones_t {
/* The number of zones including the home zone */
int n;
/* The shift of the zones with respect to the home zone */
gmx_domdec_zone_size_t size[DD_MAXZONE];
/* The cg density of the home zone */
real dens_zone0;
-} gmx_domdec_zones_t;
+};
typedef struct gmx_ga2la *gmx_ga2la_t;
typedef struct gmx_pme_comm_n_box *gmx_pme_comm_n_box_p_t;
-typedef struct {
+struct gmx_ddbox_t {
int npbcdim;
int nboundeddim;
rvec box0;
rvec v[DIM][DIM];
/* Normal vectors for the cells walls */
rvec normal[DIM];
-} gmx_ddbox_t;
+};
typedef struct {
int *ibuf; /* for ints */
int ibuf_alloc;
- gmx_large_int_t *libuf;
+ gmx_int64_t *libuf;
int libuf_alloc;
float *fbuf; /* for floats */
} mpi_in_place_buf_t;
-typedef struct {
+struct gmx_domdec_t {
/* The DD particle-particle nodes only */
/* The communication setup within the communicator all
* defined in dd->comm in domdec.c
gmx_bool pme_receive_vir_ener;
gmx_pme_comm_n_box_p_t cnb;
int nreq_pme;
- MPI_Request req_pme[4];
+ MPI_Request req_pme[8];
/* The communication setup, identical for each cell, cartesian index */
gmx_domdec_comm_p_t comm;
/* The partioning count, to keep track of the state */
- gmx_large_int_t ddp_count;
+ gmx_int64_t ddp_count;
/* gmx_pme_recv_f buffer */
int pme_recv_f_alloc;
rvec *pme_recv_f_buf;
-} gmx_domdec_t;
+};
-typedef struct gmx_partdec *gmx_partdec_p_t;
-
-typedef struct {
+struct gmx_multisim_t {
int nsim;
int sim;
MPI_Group mpi_group_masters;
/* these buffers are used as destination buffers if MPI_IN_PLACE isn't
supported.*/
mpi_in_place_buf_t *mpb;
-} gmx_multisim_t;
+};
#define DUTY_PP (1<<0)
#define DUTY_PME (1<<1)
} gmx_nodecomm_t;
-typedef struct {
+struct t_commrec {
/* The nodeids in one sim are numbered sequentially from 0.
* All communication within some simulation should happen
* in mpi_comm_mysim, or its subset mpi_comm_mygroup.
/* For domain decomposition */
gmx_domdec_t *dd;
- /* For particle decomposition */
- gmx_partdec_p_t pd;
-
/* The duties of this node, see the defines above */
int duty;
/* these buffers are used as destination buffers if MPI_IN_PLACE isn't
supported.*/
mpi_in_place_buf_t *mpb;
-} t_commrec;
+};
#define MASTERNODE(cr) (((cr)->nodeid == 0) || !PAR(cr))
/* #define MASTERTHREAD(cr) ((cr)->threadid == 0) */
#define RANK(cr, nodeid) (nodeid)
#define MASTERRANK(cr) (0)
+/* Note that even with particle decomposition removed, the use of
+ * non-DD parallelization in TPI, NM and multi-simulations means that
+ * PAR(cr) and DOMAINDECOMP(cr) are not universally synonymous. In
+ * particular, DOMAINDECOMP(cr) == true indicates that there is more
+ * than one domain, not just that the dd algorithm is active. */
#define DOMAINDECOMP(cr) (((cr)->dd != NULL) && PAR(cr))
#define DDMASTER(dd) ((dd)->rank == (dd)->masterrank)
-#define PARTDECOMP(cr) ((cr)->pd != NULL)
-
#define MULTISIM(cr) ((cr)->ms)
#define MSRANK(ms, nodeid) (nodeid)
#define MASTERSIM(ms) ((ms)->sim == 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff