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/*
*
* 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
* 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
* 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 www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
* GRoups of Organic Molecules in ACtion for Science
*/
#include "commrec.h"
#ifdef __cplusplus
extern "C" {
#endif
typedef real rvec5[5];
/* Distance restraining stuff */
typedef struct {
int dr_weighting; /* Weighting of pairs in one restraint */
gmx_bool dr_bMixed; /* Use sqrt of the instantaneous times *
* the time averaged violation */
real dr_fc; /* Force constant for disres, *
* which is multiplied by a (possibly) *
* different factor for each restraint */
real dr_tau; /* Time constant for disres */
real ETerm; /* multiplication factor for time averaging */
real ETerm1; /* 1 - ETerm1 */
real exp_min_t_tau; /* Factor for slowly switching on the force */
int nres; /* The number of distance restraints */
int npair; /* The number of distance restraint pairs */
real sumviol; /* The sum of violations */
real *rt; /* The calculated instantaneous distance (npr) */
real *rm3tav; /* The calculated time averaged distance (npr) */
real *Rtl_6; /* The calculated instantaneous r^-6 (nr) */
real *Rt_6; /* The calculated inst. ens. averaged r^-6 (nr) */
real *Rtav_6; /* The calculated time and ens. averaged r^-6 (nr) */
int nsystems; /* The number of systems for ensemble averaging */
MPI_Comm mpi_comm_ensemble; /* For ensemble averaging */
} t_disresdata;
/* Orientation restraining stuff */
typedef struct {
real fc; /* Force constant for the restraints */
real edt; /* Multiplication factor for time averaging */
real edt_1; /* 1 - edt */
real exp_min_t_tau; /* Factor for slowly switching on the force */
int nr; /* The number of orientation restraints */
int nex; /* The number of experiments */
int nref; /* The number of atoms for the fit */
real *mref; /* The masses of the reference atoms */
rvec *xref; /* The reference coordinates for the fit (nref) */
rvec *xtmp; /* Temporary array for fitting (nref) */
matrix R; /* Rotation matrix to rotate to the reference coor. */
tensor *S; /* Array of order tensors for each experiment (nexp) */
rvec5 *Dinsl; /* The order matrix D for all restraints (nr x 5) */
rvec5 *Dins; /* The ensemble averaged D (nr x 5) */
rvec5 *Dtav; /* The time and ensemble averaged D (nr x 5) */
real *oinsl; /* The calculated instantaneous orientations */
real *oins; /* The calculated emsemble averaged orientations */
real *otav; /* The calculated time and ensemble averaged orient. */
real rmsdev; /* The weighted (using kfac) RMS deviation */
rvec5 *tmp; /* An array of temporary 5-vectors (nex); */
real ***TMP; /* An array of temporary 5x5 matrices (nex); */
real *eig; /* Eigenvalues/vectors, for output only (nex x 12) */
/* variables for diagonalization with diagonalize_orires_tensors()*/
double **M;
double *eig_diag;
double **v;
} t_oriresdata;
/*
* Data struct used in the force calculation routines
* for storing the tables for bonded interactions and
* for storing information which is needed in following steps
* (for instance for time averaging in distance retraints)
* or for storing output, since force routines only return the potential.
*/
typedef struct {
bondedtable_t *bondtab;
bondedtable_t *angletab;
bondedtable_t *dihtab;
t_disresdata disres;
t_oriresdata orires;
real dihre_fc;
} t_fcdata;
#ifdef __cplusplus
}
#endif
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