src/gromacs/pbcutil/mshift.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2018, 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.
  10  *
  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.
  15  *
  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.
  20  *
  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.
  25  *
  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.
  33  *
  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.
  36  */
  37 #ifndef GMX_PBCUTIL_MSHIFT_H
  38 #define GMX_PBCUTIL_MSHIFT_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44
  45 struct InteractionList;
  46 struct gmx_moltype_t;
  47 struct t_idef;
  48
  49 typedef enum {
  50     egcolWhite, egcolGrey, egcolBlack, egcolNR
  51 } egCol;
  52
  53 struct t_graph
  54 {
  55     /* Described the connectivity between, potentially, multiple parts of
  56      * the ilist that are internally chemically bonded together.
  57      */
  58     enum class BondedParts
  59     {
  60         Single,               /* All atoms are connected through chemical bonds */
  61         MultipleDisconnected, /* There are multiple parts, e.g. monomers, that are all disconnected */
  62         MultipleConnected     /* There are multiple parts, e.g. monomers, that are partially or fully connected between each other by interactions other than chemical bonds */
  63     };
  64
  65     int          at0;       /* The first atom the graph was constructed for */
  66     int          at1;       /* The last atom the graph was constructed for  */
  67     int          nnodes;    /* The number of nodes, nnodes=at_end-at_start  */
  68     int          nbound;    /* The number of nodes with edges               */
  69     int          at_start;  /* The first connected atom in this graph       */
  70     int          at_end;    /* The last+1 connected atom in this graph      */
  71     int         *nedge;     /* For each node the number of edges            */
  72     int        **edge;      /* For each node, the actual edges (bidirect.)  */
  73     gmx_bool     bScrewPBC; /* Screw boundary conditions                    */
  74     ivec        *ishift;    /* Shift for each particle                      */
  75     int          negc;
  76     egCol       *egc;       /* color of each node */
  77     BondedParts  parts;     /* How chemically bonded parts are connected    */
  78 };
  79
  80 #define SHIFT_IVEC(g, i) ((g)->ishift[i])
  81
  82 t_graph *mk_graph(FILE *fplog,
  83                   const struct t_idef *idef, int at_start, int at_end,
  84                   gmx_bool bShakeOnly, gmx_bool bSettle);
  85 /* Build a graph from an idef description. The graph can be used
  86  * to generate mol-shift indices.
  87  * at_start and at_end should coincide will molecule boundaries,
  88  * for the whole system this is simply 0 and natoms.
  89  * If bShakeOnly, only the connections in the shake list are used.
  90  * If bSettle && bShakeOnly the settles are used too.
  91  */
  92
  93 void mk_graph_moltype(const gmx_moltype_t &moltype,
  94                       t_graph             *g);
  95 /* As mk_graph, but takes gmx_moltype_t iso t_idef and does not allocate g */
  96
  97
  98 void done_graph(t_graph *g);
  99 /* Free the memory in g */
 100
 101 void p_graph(FILE *log, const char *title, t_graph *g);
 102 /* Print a graph to log */
 103
 104 void mk_mshift(FILE *log, t_graph *g, int ePBC,
 105                const matrix box, const rvec x[]);
 106 /* Calculate the mshift codes, based on the connection graph in g. */
 107
 108 void shift_x(const t_graph *g, const matrix box, const rvec x[], rvec x_s[]);
 109 /* Add the shift vector to x, and store in x_s (may be same array as x) */
 110
 111 void shift_self(const t_graph *g, const matrix box, rvec x[]);
 112 /* Id. but in place */
 113
 114 void unshift_x(const t_graph *g, const matrix box, rvec x[], const rvec x_s[]);
 115 /* Subtract the shift vector from x_s, and store in x (may be same array) */
 116
 117 void unshift_self(const t_graph *g, const matrix box, rvec x[]);
 118 /* Id, but in place */
 119
 120 #endif