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/*
* $Id: pull.h,v 1.21 2005/03/02 14:00:33 hess Exp $
*
* 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:
* Gromacs Runs On Most of All Computer Systems
*/
#ifndef _pull_h
#define _pull_h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "vec.h"
#include "typedefs.h"
/* This file contains datatypes and function declarations necessary
for mdrun to interface with the pull code */
typedef enum {
eAfm, eConstraint, eUmbrella, ePullruntypeNR
} t_pullruntype;
typedef enum {
eCom, eComT0, eDyn, eDynT0
} t_pullreftype;
typedef struct {
atom_id *idx; /* indices of pull atoms in full coordinate array */
int nweight; /* The number of weights read from the param file */
real *weight; /* weights (use all 1 when nweight==0) */
int ngx; /* pull group size */
char *name; /* pull group name */
real wscale; /* scaling factor for the weights: sum w m/sum w w m */
real invtm; /* inverse total mass of the group: 1/wscale sum w m */
rvec *x0; /* pull group coordinates at t=0 */
rvec *xp; /* pull group coordinates at previous step */
dvec x_ref; /* reference position */
dvec x_unc; /* center of mass before constraining */
dvec x_con; /* center of mass, obeying constraints */
dvec xprev; /* position of coms in last written structure */
dvec f; /* force due to the pulling/constraining */
dvec spring; /* coordinates of the spring (eAfm) */
dvec dir; /* direction of constraint */
real constr_d0;/* reference distance of constraint (nm) */
real constr_rate;/* rate of change of the constraint length (nm/ps) */
dvec xtarget; /* target coordinates for structure generation */
dvec *comhist; /* com over the last nhist steps (for running aver) */
dvec AfmVec; /* Vector to pull along for AFM */
real AfmK; /* Force constant to use for AFM */
real AfmRate; /* Pull rate in nm/ps */
dvec AfmInit; /* Initial sprint posistions for AFM */
dvec UmbPos; /* center of umbrella potential */
real UmbCons; /* force constant of umbrella potential */
} t_pullgrp;
typedef struct {
t_pullgrp ref; /* reference group, reaction force grps */
int ngrp; /* number of groups */
t_pullgrp *grp; /* groups to pull/restrain/etc/ */
t_pullgrp *dyna; /* dynamic groups for use with local constraints */
t_pullruntype runtype; /* start, afm, constraint, umbrella, test */
t_pullreftype reftype; /* com, com_t0, dynamic, dynamic_t0 */
ivec dims; /* used to select components for constraint */
int bDir; /* use only the direction dir */
dvec dir; /* direction */
real r; /* radius of cylinder for dynamic COM */
real rc; /* radius of cylinder including switch length */
real constr_tol; /* absolute tolerance for constraints in (nm) */
bool bPull; /* true if we're doing any pulling */
bool bCyl; /* true if we're using dynamic ref. groups */
FILE *out; /* output file for pull data */
int update; /* update frequency for dynamic grps */
int reflag; /* running average over reflag steps for com */
bool AbsoluteRef; /* Reference is in absolute coordinates */
bool bVerbose; /* be loud and noise */
int nSkip; /* only write output every nSkip steps */
} t_pull;
/* main pull routine that controls all the action */
extern void pull(t_pull *pull, /* all pull data */
rvec *x, /* coordinates, changed by constraint run */
rvec *f, /* forces, changed by Afm run */
tensor vir, /* the virial */
matrix box,
t_topology *top, /* needed to write out coordinate files */
real dt, /* time step */
int step, /* step number in simulation */
real time, /* time, only used for printing output */
t_mdatoms *md, /* masses and charges of all atoms */
int start, /* number of first atom belonging to this node */
int homenr, /* number of atoms that belong to this node */
t_commrec * cr /* Stuff for communication */
);
/* get memory and initialize the fields of pull that still need it, and
do runtype specific initialization */
extern void init_pull(FILE *log,
int nfile,
t_filenm fnm[], /* standard filename struct */
t_pull *pull, /* all pull data */
rvec *x, /* all coordinates */
t_mdatoms *md, /* masses and charges of all atoms */
ivec nFreeze[], /* the freeze dimensions */
matrix box,
int start, /* startinig index of this node */
int homenr, /* number of atoms on this node */
t_commrec * cr /* struct for communication info */
);
#endif
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