2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
37 /* This file is completely threadsafe - keep it that way! */
43 #include "gromacs/utility/smalloc.h"
44 #include "types/commrec.h"
47 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/utility/futil.h"
52 #include "gromacs/fileio/gmxfio.h"
54 #define header "Neighborlist:"
56 static void write_nblist(FILE *out
, gmx_domdec_t
*dd
, t_nblist
*nblist
, int nDNL
)
58 int i
, nii
, ii
, j
, zi
, zj0
, zj1
, aj
, zj
, nj
;
59 int ca1
[DD_MAXZONE
], np
[DD_MAXZONE
];
60 gmx_domdec_zones_t
*dd_zones
;
64 fprintf(out
, "ielec: %d, ivdw: %d, type: %d, Solvent opt: %s\n",
65 nblist
->ielec
, nblist
->ivdw
, nblist
->type
,
66 gmx_nblist_geometry_names
[nblist
->igeometry
]);
67 fprintf(out
, "nri: %d npair: %d\n", nblist
->nri
, nblist
->nrj
);
70 dd_zones
= domdec_zones(dd
);
72 for (zi
= 0; zi
< dd_zones
->n
; zi
++)
74 ca1
[zi
] = dd
->cgindex
[dd_zones
->cg_range
[zi
+1]];
77 for (zi
= 0; zi
< dd_zones
->nizone
; zi
++)
79 zj0
= dd_zones
->izone
[zi
].j0
;
80 zj1
= dd_zones
->izone
[zi
].j1
;
81 for (zj
= zj0
; zj
< zj1
; zj
++)
85 while (i
< nblist
->nri
&& nblist
->iinr
[i
] < ca1
[zi
])
87 for (j
= nblist
->jindex
[i
]; (j
< nblist
->jindex
[i
+1]); j
++)
99 fprintf(out
, "DD zone %d:", zi
);
100 for (zj
= zj0
; zj
< zj1
; zj
++)
102 fprintf(out
, " %d %d", zj
, np
[zj
]);
109 for (i
= 0; i
< nblist
->nri
; i
++)
112 if (nDNL
>= 3 && nblist
->igeometry
!= GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE
)
116 nj
= nblist
->jindex
[i
+1] - nblist
->jindex
[i
];
117 fprintf(out
, "i: %d shift: %d gid: %d nj: %d\n",
118 ddglatnr(dd
, nblist
->iinr
[i
]),
119 nblist
->shift
[i
], nblist
->gid
[i
], nj
);
120 for (ii
= 0; ii
< nii
; ii
++)
122 for (j
= nblist
->jindex
[i
]; (j
< nblist
->jindex
[i
+1]); j
++)
124 fprintf(out
, " i: %5d j: %5d\n",
125 ddglatnr(dd
, nblist
->iinr
[i
]+ii
),
126 ddglatnr(dd
, nblist
->jjnr
[j
]));
135 static void set_mat(FILE *fp
, int **mat
, int i0
, int ni
, int j0
, int nj
,
136 gmx_bool bSymm
, int shift
)
140 for (i
= i0
; (i
< i0
+ni
); i
++)
142 for (j
= j0
; (j
< j0
+nj
); j
++)
146 fprintf(fp
, "mat[%d][%d] changing from %d to %d\n",
147 i
, j
, mat
[i
][j
], shift
+1);
152 mat
[j
][i
] = 27-shift
;
160 void dump_nblist(FILE *out
, t_commrec
*cr
, t_forcerec
*fr
, int nDNL
)
163 static FILE *fp
= NULL
;
171 sprintf(buf
, "nlist_n%d.txt", cr
->nodeid
);
175 sprintf(buf
, "nlist.txt");
177 fp
= gmx_fio_fopen(buf
, "w");
179 fprintf(fp
, "%s\n", header
);
181 for (n
= 0; (n
< fr
->nnblists
); n
++)
183 for (i
= 0; (i
< eNL_NR
); i
++)
185 write_nblist(fp
, cr
->dd
, &fr
->nblists
[n
].nlist_sr
[i
], nDNL
);
192 fprintf(out
, "%s\n", header
);
194 for (n
= 0; (n
< fr
->nnblists
); n
++)
196 for (i
= 0; (i
< eNL_NR
); i
++)
198 write_nblist(out
, cr
->dd
, &fr
->nblists
[n
].nlist_sr
[i
], nDNL
);