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/*
* $Id$
*
* 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
*/
#ifdef HAVE_CONFIG_H
#include<config.h>
#endif
#include "typedefs.h"
enum { econqCoord, /* Constrain coordinates (mass weighted) */
econqVeloc, /* Constrain velocities (mass weighted) */
econqDeriv, /* Constrain a derivative (mass weighted), *
* for instance velocity or acceleration, *
* constraint virial can not be calculated. */
econqDeriv_FlexCon, /* As econqDeriv, but only output flex. con. */
econqForce /* Constrain forces (non mass-weighted) */
};
extern int n_flexible_constraints(struct gmx_constr *constr);
/* Returns the total number of flexible constraints in the system */
extern void too_many_constraint_warnings(int eConstrAlg,int warncount);
/* Generate a fatal error because of too many LINCS/SETTLE warnings */
extern bool bshakef(FILE *log, /* Log file */
int natoms, /* Total number of atoms */
real invmass[], /* Atomic masses */
int nblocks, /* The number of shake blocks */
int sblock[], /* The shake blocks */
t_idef *idef, /* The interaction def */
t_inputrec *ir, /* Input record */
matrix box, /* The box */
rvec x_s[], /* Coords before update */
rvec xp[], /* Output coords */
t_nrnb *nrnb, /* Performance measure */
real *lagr, /* The Lagrange multipliers */
real lambda, /* FEP lambda */
real *dvdlambda, /* FEP force */
real invdt, /* 1/delta_t */
rvec *v, /* Also constrain v if v!=NULL */
bool bCalcVir, /* Calculate r x m delta_r */
tensor rmdr, /* sum r x m delta_r */
bool bDumpOnError); /* Dump debugging stuff on error*/
/* Shake all the atoms blockwise. It is assumed that all the constraints
* in the idef->shakes field are sorted, to ascending block nr. The
* sblock array points into the idef->shakes.iatoms field, with block 0
* starting
* at sblock[0] and running to ( < ) sblock[1], block n running from
* sblock[n] to sblock[n+1]. Array sblock should be large enough.
* Return TRUE when OK, FALSE when shake-error
*/
extern void csettle(FILE *log,
int nsettle, /* Number of settles */
t_iatom iatoms[], /* The settle iatom list */
real b4[], /* Old coordinates */
real after[], /* New coords, to be settled */
real dOH, /* Constraint length Ox-Hyd */
real dHH, /* Constraint length Hyd-Hyd */
real mO, /* Mass of Oxygen */
real mH, /* Mass of Hydrogen */
real invdt, /* 1/delta_t */
real *v, /* Also constrain v if v!=NULL */
bool bCalcVir, /* Calculate r x m delta_r */
tensor rmdr, /* sum r x m delta_r */
int *xerror);
extern void settle_proj(FILE *fp,int nsettle, t_iatom iatoms[],rvec x[],
real dOH,real dHH,real invmO,real invmH,
rvec *der,rvec *derp,
bool bCalcVir,tensor rmdder);
/* Analytical algorithm to subtract the components of derivatives
* of coordinates working on settle type constraint.
*/
extern void cshake(atom_id iatom[],int ncon,int *nnit,int maxnit,
real dist2[],real xp[],real rij[],real m2[],real omega,
real invmass[],real tt[],real lagr[],int *nerror);
/* Regular iterative shake */
extern bool constrain(FILE *log,bool bLog,bool bEner,
gmx_constr_t constr,
t_idef *idef,
t_inputrec *ir,
t_commrec *cr,
int step,int delta_step,
t_mdatoms *md,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,
rvec *v,tensor *vir,
t_nrnb *nrnb,int econq);
/*
* When econq=econqCoord constrains coordinates xprime using th
* directions in x, min_proj is not used.
*
* When econq=econqDeriv, calculates the components xprime in
* the constraint directions and subtracts these components from min_proj.
* So when min_proj=xprime, the constraint components are projected out.
*
* When econq=econqDeriv_FlexCon, the same is done as with econqDeriv,
* but only the components of the flexible constraints are stored.
*
* delta_step is used for determining the constraint reference lengths
* when lenA != lenB or will the pull code with a pulling rate.
* step + delta_step is the step at which the final configuration
* is meant to be; for update delta_step = 1.
*
* If v!=NULL also constrain v by adding the constraint corrections / dt.
*
* If vir!=NULL calculate the constraint virial.
*
* Init_constraints must have be called once, before calling constrain.
*
* Return TRUE if OK, FALSE in case of shake error
*
*/
extern gmx_constr_t init_constraints(FILE *log,
gmx_mtop_t *mtop,t_inputrec *ir,
gmx_edsam_t ed,t_state *state,
t_commrec *cr);
/* Initialize constraints stuff */
extern void set_constraints(gmx_constr_t constr,
gmx_localtop_t *top,
t_inputrec *ir,
t_mdatoms *md,
gmx_domdec_t *dd);
/* Set up all the local constraints for the node */
extern t_blocka make_at2con(int start,int natoms,
t_ilist *ilist,t_iparams *iparams,
bool bDynamics,int *nflexiblecons);
/* Returns a block struct to go from atoms to constraints */
extern t_blocka *atom2constraints_moltype(gmx_constr_t constr);
/* Returns the an arry of atom to constraints lists for the moltypes */
extern bool inter_charge_group_constraints(gmx_mtop_t *mtop);
/* Returns if there are inter charge group constraints */
extern real *constr_rmsd_data(gmx_constr_t constr);
/* Return the data for determining constraint RMS relative deviations.
* Returns NULL when LINCS is not used.
*/
extern real constr_rmsd(gmx_constr_t constr,bool bSD2);
/* Return the RMSD of the constraint, bSD2 selects the second SD step */
extern real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
/* Return the data for determining constraint RMS relative deviations */
extern real lincs_rmsd(gmx_lincsdata_t lincsd,bool bSD2);
/* Return the RMSD of the constraint, bSD2 selects the second SD step */
gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
int nflexcon_global,t_blocka *at2con,
bool bPLINCS,int nIter,int nProjOrder);
/* Initializes and returns the lincs data struct */
extern void set_lincs(t_idef *idef,t_mdatoms *md,
bool bDynamics,gmx_domdec_t *dd,
gmx_lincsdata_t li);
/* Initialize lincs stuff */
extern void set_lincs_matrix(gmx_lincsdata_t li,real *invmass,real lambda);
/* Sets the elements of the LINCS constraint coupling matrix */
extern real constr_r_max(FILE *fplog,gmx_mtop_t *mtop,t_inputrec *ir);
/* Returns an estimate of the maximum distance between atoms
* required for LINCS.
*/
extern bool constrain_lincs(FILE *log,bool bLog,bool bEner,
t_inputrec *ir,
int step,gmx_lincsdata_t lincsd,t_mdatoms *md,
gmx_domdec_t *dd,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,
real invdt,rvec *v,
bool bCalcVir,tensor rmdr,
int econ,
t_nrnb *nrnb,
int maxwarn,int *warncount);
/* Returns if the constraining succeeded */
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