src/gromacs/mdtypes/fcdata.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) 2012,2014,2015,2016,2017, 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_MDTYPES_FCDATA_H
  38 #define GMX_MDTYPES_FCDATA_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/topology/idef.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43 #include "gromacs/utility/real.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 typedef real rvec5[5];
  50
  51 /* Distance restraining stuff */
  52 typedef struct t_disresdata {
  53     int      dr_weighting; /* Weighting of pairs in one restraint              */
  54     gmx_bool dr_bMixed;    /* Use sqrt of the instantaneous times              *
  55                             * the time averaged violation                      */
  56     real     dr_fc;        /* Force constant for disres,                       *
  57                             * which is multiplied by a (possibly)              *
  58                             * different factor for each restraint              */
  59     real  dr_tau;          /* Time constant for disres                    */
  60     real  ETerm;           /* multiplication factor for time averaging         */
  61     real  ETerm1;          /* 1 - ETerm1                                       */
  62     real  exp_min_t_tau;   /* Factor for slowly switching on the force         */
  63     int   nres;            /* The number of distance restraints                */
  64     int   npair;           /* The number of distance restraint pairs           */
  65     int   type_min;        /* The minimum iparam type index for restraints     */
  66     real  sumviol;         /* The sum of violations                            */
  67     real *rt;              /* The instantaneous distance (npair)               */
  68     real *rm3tav;          /* The time averaged distance (npair)               */
  69     real *Rtl_6;           /* The instantaneous r^-6 (nres)                    */
  70     real *Rt_6;            /* The instantaneous ensemble averaged r^-6 (nres)  */
  71     real *Rtav_6;          /* The time and ensemble averaged r^-6 (nres)       */
  72     int   nsystems;        /* The number of systems for ensemble averaging     */
  73
  74     /* TODO: Implement a proper solution for parallel disre indexing */
  75     const t_iatom *forceatomsStart; /* Pointer to the start of the disre forceatoms */
  76 } t_disresdata;
  77
  78 /* All coefficients for the matrix equation for the orientation tensor */
  79 struct OriresMatEq
  80 {
  81     real rhs[5];    /* The right hand side of the matrix equation */
  82     real mat[5][5]; /* The matrix                                 */
  83 };
  84
  85 /* Orientation restraining stuff */
  86 typedef struct t_oriresdata {
  87     real         fc;            /* Force constant for the restraints                  */
  88     real         edt;           /* Multiplication factor for time averaging           */
  89     real         edt_1;         /* 1 - edt                                            */
  90     real         exp_min_t_tau; /* Factor for slowly switching on the force         */
  91     int          nr;            /* The number of orientation restraints               */
  92     int          nex;           /* The number of experiments                          */
  93     int          typeMin;       /* The minimum iparam type index for restraints       */
  94     int          nref;          /* The number of atoms for the fit                    */
  95     real        *mref;          /* The masses of the reference atoms                  */
  96     rvec        *xref;          /* The reference coordinates for the fit (nref)       */
  97     rvec        *xtmp;          /* Temporary array for fitting (nref)                 */
  98     matrix       R;             /* Rotation matrix to rotate to the reference coor.   */
  99     tensor      *S;             /* Array of order tensors for each experiment (nexp)  */
 100     rvec5       *Dinsl;         /* The order matrix D for all restraints (nr x 5)     */
 101     rvec5       *Dins;          /* The ensemble averaged D (nr x 5)                   */
 102     rvec5       *Dtav;          /* The time and ensemble averaged D (nr x 5)          */
 103     real        *oinsl;         /* The calculated instantaneous orientations          */
 104     real        *oins;          /* The calculated emsemble averaged orientations      */
 105     real        *otav;          /* The calculated time and ensemble averaged orient.  */
 106     real         rmsdev;        /* The weighted (using kfac) RMS deviation            */
 107     OriresMatEq *tmpEq;         /* An temporary array of matrix + rhs                 */
 108     real        *eig;           /* Eigenvalues/vectors, for output only (nex x 12)    */
 109
 110     /* variables for diagonalization with diagonalize_orires_tensors()*/
 111     double **M;
 112     double  *eig_diag;
 113     double **v;
 114 } t_oriresdata;
 115
 116 typedef struct bondedtable_t {
 117     int   n;      /* n+1 is the number of points */
 118     real  scale;  /* distance between two points */
 119     real *data;   /* the actual table data, per point there are 4 numbers */
 120 } bondedtable_t;
 121
 122 /*
 123  * Data struct used in the force calculation routines
 124  * for storing the tables for bonded interactions and
 125  * for storing information which is needed in following steps
 126  * (for instance for time averaging in distance retraints)
 127  * or for storing output, since force routines only return the potential.
 128  */
 129 typedef struct t_fcdata {
 130     bondedtable_t *bondtab;
 131     bondedtable_t *angletab;
 132     bondedtable_t *dihtab;
 133
 134     t_disresdata   disres;
 135     t_oriresdata   orires;
 136 } t_fcdata;
 137
 138 #ifdef __cplusplus
 139 }
 140 #endif
 141
 142 #endif