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lincs.h File Reference
#include <cstdio>
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+ Include dependency graph for lincs.h:


Declares interface to LINCS code.

Berk Hess
Mark Abraham


class  gmx::ArrayRefWithPadding< typename >
 Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses. More...
class  gmx::ArrayRef< typename >
 STL-like interface to a C array of T (or part of a std container of T). More...
class  gmx::ListOfLists< typename >
 A list of lists, optimized for performance. More...


real gmx::lincs_rmsd (const Lincs *lincsd)
 Return the RMSD of the constraint.
Lincs * gmx::init_lincs (FILE *fplog, const gmx_mtop_t &mtop, int nflexcon_global, ArrayRef< const ListOfLists< int >> atomsToConstraintsPerMolType, bool bPLINCS, int nIter, int nProjOrder, ObservablesReducerBuilder *observablesReducerBuilder)
 Initializes and returns the lincs data struct.
void gmx::done_lincs (Lincs *li)
 Destructs the lincs object when it is not nullptr.
void gmx::set_lincs (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass, real lambda, bool bDynamics, const t_commrec *cr, Lincs *li)
 Initialize lincs stuff.
bool gmx::constrain_lincs (bool computeRmsd, const t_inputrec &ir, int64_t step, Lincs *lincsd, ArrayRef< const real > invmass, const t_commrec *cr, const gmx_multisim_t *ms, ArrayRefWithPadding< const RVec > x, ArrayRefWithPadding< RVec > xprime, ArrayRef< RVec > min_proj, const matrix box, t_pbc *pbc, bool hasMassPerturbed, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq, t_nrnb *nrnb, int maxwarn, int *warncount, gmx_wallcycle *wcycle)
 Applies LINCS constraints. More...