/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014, 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.
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*/
-
-#include "commrec.h"
+#ifndef _fcdata_h
+#define _fcdata_h
#ifdef __cplusplus
extern "C" {
#endif
+#include "gromacs/math/vectypes.h"
+
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 */
+ 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 */
} 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) */
+ 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;
+ /* variables for diagonalization with diagonalize_orires_tensors()*/
+ double **M;
+ double *eig_diag;
+ double **v;
} t_oriresdata;
-/*
+typedef struct {
+ int n; /* n+1 is the number of points */
+ real scale; /* distance between two points */
+ real *data; /* the actual table data, per point there are 4 numbers */
+} bondedtable_t;
+
+/*
* 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
* or for storing output, since force routines only return the potential.
*/
typedef struct {
- bondedtable_t *bondtab;
- bondedtable_t *angletab;
- bondedtable_t *dihtab;
+ bondedtable_t *bondtab;
+ bondedtable_t *angletab;
+ bondedtable_t *dihtab;
- t_disresdata disres;
- t_oriresdata orires;
- real dihre_fc;
+ t_disresdata disres;
+ t_oriresdata orires;
} t_fcdata;
#ifdef __cplusplus
}
#endif
+#endif /* _fcdata_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff