constr.cpp File Reference

#include "gmxpre.h"
#include "constr.h"
#include <cassert>
#include <cmath>
#include <cstdlib>
#include <algorithm>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/lincs.h"
#include "gromacs/mdlib/settle.h"
#include "gromacs/mdlib/shake.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/txtdump.h"

Include dependency graph for constr.cpp:

Description

Defines the high-level constraint code.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

Functions
static void	gmx::clear_constraint_quantity_nonlocal (const gmx_domdec_t &dd, ArrayRef< RVec > q)
	Clears constraint quantities for atoms in nonlocal region.
void	gmx::too_many_constraint_warnings (ConstraintAlgorithm eConstrAlg, int warncount)
	Generate a fatal error because of too many LINCS/SETTLE warnings.
static void	gmx::write_constr_pdb (const char *fn, const char *title, const gmx_mtop_t &mtop, int start, int homenr, const t_commrec *cr, ArrayRef< const RVec > x, const matrix box)
	Writes out coordinates.
static void	gmx::dump_confs (FILE *log, int64_t step, const gmx_mtop_t &mtop, int start, int homenr, const t_commrec *cr, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, const matrix box)
	Writes out domain contents to help diagnose crashes.
FlexibleConstraintTreatment	gmx::flexibleConstraintTreatment (bool haveDynamicsIntegrator)
	Returns the flexible constraint treatment depending on whether the integrator is dynamic.
static ListOfLists< int >	gmx::makeAtomsToConstraintsList (int numAtoms, ArrayRef< const InteractionList > ilists, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a block struct to go from atoms to constraints. More...
ListOfLists< int >	gmx::make_at2con (int numAtoms, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
ListOfLists< int >	gmx::make_at2con (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
int	gmx::countFlexibleConstraints (ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams)
	Return the number of flexible constraints in the ilist and iparams.
static std::vector< int >	gmx::make_at2settle (int natoms, const InteractionList &ilist)
	Returns the index of the settle to which each atom belongs.
static std::vector < ListOfLists< int > >	gmx::makeAtomToConstraintMappings (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Makes a per-moleculetype container of mappings from atom indices to constraint indices. More...
bool	gmx::hasTriangleConstraints (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns True if there is at least one triangular constraint.
void	gmx::do_constrain_first (FILE *log, gmx::Constraints *constr, const t_inputrec *inputrec, int numAtoms, int numHomeAtoms, ArrayRefWithPadding< RVec > x, ArrayRefWithPadding< RVec > v, const matrix box, real lambda)
	Constrain the initial coordinates and velocities.
void	gmx::constrain_velocities (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
	Constrain velocities only. More...
void	gmx::constrain_coordinates (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, ArrayRefWithPadding< RVec > xp, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
	Constraint coordinates. More...