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#ifndef _constr_h
#define _constr_h
-#include "typedefs.h"
-#include "types/commrec.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_pbc;
+
enum
{
- econqCoord, /* Constrain coordinates (mass weighted) */
+ econqCoord, /* Constrain coordinates (mass weighted) */
econqVeloc, /* Constrain velocities (mass weighted) */
econqDeriv, /* Constrain a derivative (mass weighted), *
* for instance velocity or acceleration, *
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);
+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 */
+gmx_bool bshakef(FILE *log, /* Log file */
+ gmx_shakedata_t shaked, /* 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
+ * 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
+ * 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);
+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,
+void csettle(gmx_settledata_t settled,
+ int nsettle, /* Number of settles */
+ t_iatom iatoms[], /* The settle iatom list */
+ const struct 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(gmx_settledata_t settled, int econq,
int nsettle, t_iatom iatoms[],
- const t_pbc *pbc, /* PBC data pointer, can be NULL */
+ const struct t_pbc *pbc, /* PBC data pointer, can be NULL */
rvec x[],
- rvec *der,rvec *derp,
- int CalcVirAtomEnd,tensor vir_r_m_dder,
+ 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);
+void cshake(const atom_id iatom[], int ncon, int *nnit, int maxnit,
+ const real dist2[], real xp[], const real rij[], const real m2[], real omega,
+ const real invmass[], const 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);
+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_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,
+ gmx_int64_t step, int delta_step,
+ real step_scaling,
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);
+ 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.
* step + delta_step is the step at which the final configuration
* is meant to be; for update delta_step = 1.
*
+ * step_scaling can be used to update coordinates based on the time
+ * step multiplied by this factor. Thus, normally 1.0 is passed. The
+ * SD1 integrator uses 0.5 in one of its calls, to correct positions
+ * for half a step of changed velocities.
+ *
* 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
+ * 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.
*
*/
gmx_constr_t init_constraints(FILE *log,
- gmx_mtop_t *mtop,t_inputrec *ir,
- gmx_edsam_t ed,t_state *state,
- t_commrec *cr);
+ gmx_mtop_t *mtop, t_inputrec *ir,
+ gmx_edsam_t ed, t_state *state,
+ t_commrec *cr);
/* Initialize constraints stuff */
-void set_constraints(gmx_constr_t constr,
- gmx_localtop_t *top,
- t_inputrec *ir,
- t_mdatoms *md,
- t_commrec *cr);
+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
* after the F_CONSTR constraints.
*/
-t_blocka make_at2con(int start,int natoms,
- t_ilist *ilist,t_iparams *iparams,
- gmx_bool bDynamics,int *nflexiblecons);
+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);
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)
+#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.
* Returns NULL when LINCS is not used.
*/
-real constr_rmsd(gmx_constr_t constr,gmx_bool bSD2);
+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);
+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);
+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);
+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);
+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);
+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,
+constrain_lincs(FILE *log, gmx_bool bLog, gmx_bool bEner,
+ t_inputrec *ir,
+ gmx_int64_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);
+ rvec *x, rvec *xprime, rvec *min_proj,
+ matrix box, struct 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 */
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