gromacs-dev 4.6.5-1build1 / usr / include / gromacs / constr.h

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#ifndef _constr_h
#define _constr_h
#include "visibility.h"
#include "typedefs.h"
#include "types/commrec.h"

#ifdef __cplusplus
extern "C" {
#endif

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)            */
    econqForceDispl     /* Constrain forces (mass-weighted 1/0 for freeze) */
};

GMX_LIBMD_EXPORT
int n_flexible_constraints(struct gmx_constr *constr);
/* Returns the total number of flexible constraints in the system */

void too_many_constraint_warnings(int eConstrAlg, int warncount);
/* Generate a fatal error because of too many LINCS/SETTLE warnings */

gmx_shakedata_t shake_init();
/* Initializes and return the SHAKE data structure */

gmx_bool bshakef(FILE           *log,          /* Log file			*/
                 gmx_shakedata_t shaked,       /* SHAKE data */
                 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		        */
                 rvec            x_s[],        /* Coords before update		*/
                 rvec            prime[],      /* 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  */
                 gmx_bool        bCalcVir,     /* Calculate r x m delta_r      */
                 tensor          vir_r_m_dr,   /* sum r x m delta_r            */
                 gmx_bool        bDumpOnError, /* Dump debugging stuff on error*/
                 int             econq,        /* which type of constrainint is occurring */
                 t_vetavars     *vetavar);     /* veta for pressure control */
/* 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
 */

gmx_settledata_t settle_init(real mO, real mH, real invmO, real invmH,
                             real dOH, real dHH);
/* Initializes and returns a structure with SETTLE parameters */

void csettle(gmx_settledata_t settled,
             int              nsettle,          /* Number of settles            */
             t_iatom          iatoms[],         /* The settle iatom list        */
             const t_pbc     *pbc,              /* PBC data pointer, can be NULL  */
             real             b4[],             /* Old coordinates		*/
             real             after[],          /* New coords, to be settled	*/
             real             invdt,            /* 1/delta_t                    */
             real            *v,                /* Also constrain v if v!=NULL  */
             int              calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
             tensor           vir_r_m_dr,       /* sum r x m delta_r            */
             int             *xerror,
             t_vetavars      *vetavar           /* variables for pressure control */
             );

void settle_proj(FILE *fp,
                 gmx_settledata_t settled, int econq,
                 int nsettle, t_iatom iatoms[],
                 const t_pbc *pbc,   /* PBC data pointer, can be NULL  */
                 rvec x[],
                 rvec *der, rvec *derp,
                 int CalcVirAtomEnd, tensor vir_r_m_dder,
                 t_vetavars *vetavar);
/* Analytical algorithm to subtract the components of derivatives
 * of coordinates working on settle type constraint.
 */

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 */

void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
             real dist2[], real vp[], real rij[], real m2[], real omega,
             real invmass[], real tt[], real lagr[], int *nerror, real invdt, t_vetavars *vetavar);

gmx_bool constrain(FILE *log, gmx_bool bLog, gmx_bool bEner,
                   gmx_constr_t constr,
                   t_idef *idef,
                   t_inputrec *ir,
                   gmx_ekindata_t *ekind,
                   t_commrec *cr,
                   gmx_large_int_t step, int delta_step,
                   t_mdatoms *md,
                   rvec *x, rvec *xprime, rvec *min_proj,
                   gmx_bool bMolPBC, matrix box,
                   real lambda, real *dvdlambda,
                   rvec *v, tensor *vir,
                   t_nrnb *nrnb, int econq, gmx_bool bPscal, real veta, real vetanew);
/*
 * 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.
 *
 * When bMolPBC=TRUE, assume that molecules might be broken: correct PBC.
 *
 * 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.
 *
 * if veta != NULL, constraints are done assuming isotropic pressure control
 * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
 *
 * Init_constraints must have be called once, before calling constrain.
 *
 * Return TRUE if OK, FALSE in case of shake error
 *
 */

GMX_LIBMD_EXPORT
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 */

GMX_LIBMD_EXPORT
void set_constraints(gmx_constr_t    constr,
                     gmx_localtop_t *top,
                     t_inputrec     *ir,
                     t_mdatoms      *md,
                     t_commrec      *cr);
/* Set up all the local constraints for the node */

/* The at2con t_blocka struct returned by the routines below
 * contains a list of constraints per atom.
 * The F_CONSTRNC constraints in this structure number consecutively
 * after the F_CONSTR constraints.
 */

t_blocka make_at2con(int start, int natoms,
                     t_ilist *ilist, t_iparams *iparams,
                     gmx_bool bDynamics, int *nflexiblecons);
/* Returns a block struct to go from atoms to constraints */

const t_blocka *atom2constraints_moltype(gmx_constr_t constr);
/* Returns the an array of atom to constraints lists for the moltypes */

const int **atom2settle_moltype(gmx_constr_t constr);
/* Returns the an array of atom to settle for the moltypes */

#define constr_iatomptr(nconstr, iatom_constr, iatom_constrnc, con) ((con) < (nconstr) ? (iatom_constr)+(con)*3 : (iatom_constrnc)+(con-nconstr)*3)
/* Macro for getting the constraint iatoms for a constraint number con
 * which comes from a list where F_CONSTR and F_CONSTRNC constraints
 * are concatenated.
 */

gmx_bool inter_charge_group_constraints(const gmx_mtop_t *mtop);
/* Returns if there are inter charge group constraints */

gmx_bool inter_charge_group_settles(const gmx_mtop_t *mtop);
/* Returns if there are inter charge group settles */

real *constr_rmsd_data(gmx_constr_t constr);
/* Return the data for determining constraint RMS relative deviations.
 * Returns NULL when LINCS is not used.
 */

GMX_LIBMD_EXPORT
real constr_rmsd(gmx_constr_t constr, gmx_bool bSD2);
/* Return the RMSD of the constraint, bSD2 selects the second SD step */

real *lincs_rmsd_data(gmx_lincsdata_t lincsd);
/* Return the data for determining constraint RMS relative deviations */

real lincs_rmsd(gmx_lincsdata_t lincsd, gmx_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,
                           gmx_bool bPLINCS, int nIter, int nProjOrder);
/* Initializes and returns the lincs data struct */

void set_lincs(t_idef *idef, t_mdatoms *md,
               gmx_bool bDynamics, t_commrec *cr,
               gmx_lincsdata_t li);
/* Initialize lincs stuff */

void set_lincs_matrix(gmx_lincsdata_t li, real *invmass, real lambda);
/* Sets the elements of the LINCS constraint coupling matrix */

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.
 */

gmx_bool
constrain_lincs(FILE *log, gmx_bool bLog, gmx_bool bEner,
                t_inputrec *ir,
                gmx_large_int_t step,
                gmx_lincsdata_t lincsd, t_mdatoms *md,
                t_commrec *cr,
                rvec *x, rvec *xprime, rvec *min_proj,
                matrix box, t_pbc *pbc,
                real lambda, real *dvdlambda,
                real invdt, rvec *v,
                gmx_bool bCalcVir, tensor vir_r_m_dr,
                int econ,
                t_nrnb *nrnb,
                int maxwarn, int *warncount);
/* Returns if the constraining succeeded */


/* helper functions for andersen temperature control, because the
 * gmx_constr construct is only defined in constr.c. Return the list
 * of blocks (get_sblock) and the number of blocks (get_nblocks).  */

int *get_sblock(struct gmx_constr *constr);

int get_nblocks(struct gmx_constr *constr);

#ifdef __cplusplus
}
#endif
#endif