#include "gmxpre.h"
#include "lincs.h"
#include "config.h"
#include <cassert>
#include <cinttypes>
#include <climits>
#include <cmath>
#include <cstdint>
#include <cstdlib>
#include <algorithm>
#include <array>
#include <filesystem>
#include <functional>
#include <memory>
#include <optional>
#include <string>
#include <type_traits>
#include <utility>
#include <vector>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/observablesreducer.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_simd.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/alignedallocator.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/stringutil.h"

Include dependency graph for lincs.cpp:

Description

Defines LINCS 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

Classes
struct	anonymous_namespace{lincs.cpp}::AtomPair
	Indices of the two atoms involved in a single constraint. More...

struct	anonymous_namespace{lincs.cpp}::Task
	Unit of work within LINCS. More...

class	gmx::Lincs
	Data for LINCS algorithm. More...

struct	gmx::LincsDeviations
	Status information about how well LINCS satisfied the constraints in this domain. More...

Functions
real	gmx::lincs_rmsd (const Lincs *lincsd)
	Return the RMSD of the constraint.

static void	gmx::lincs_matrix_expand (const Lincs &lincsd, const Task &li_task, gmx::ArrayRef< const real > blcc, gmx::ArrayRef< real > rhs1, gmx::ArrayRef< real > rhs2, gmx::ArrayRef< real > sol)
	Do a set of nrec LINCS matrix multiplications. More...

static void	gmx::lincs_update_atoms_noind (int ncons, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update atomic coordinates when an index is not required.

static void	gmx::lincs_update_atoms_ind (gmx::ArrayRef< const int > ind, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update atomic coordinates when an index is required.

static void	gmx::lincs_update_atoms (Lincs li, int th, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec x)
	Update coordinates for atoms.

static void	gmx::do_lincsp (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > fPadded, ArrayRef< RVec > fp, t_pbc pbc, Lincs lincsd, int th, ArrayRef< const real > invmass, ConstraintVariable econq, bool bCalcDHDL, bool bCalcVir, tensor rmdf)
	LINCS projection, works on derivatives of the coordinates.

static gmx_unused void	gmx::calc_dist_iter (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec gmx_restrict xp, const real gmx_restrict bllen, const real gmx_restrict blc, const t_pbc pbc, real wfac, real gmx_restrict rhs, real gmx_restrict sol, bool *bWarn)
	Determine the distances and right-hand side for the next iteration.

static void	gmx::do_lincs (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > xpPadded, const matrix box, t_pbc pbc, Lincs lincsd, int th, ArrayRef< const real > invmass, const t_commrec cr, bool bCalcDHDL, real wangle, bool bWarn, real invdt, ArrayRef< RVec > vRef, bool bCalcVir, tensor vir_r_m_dr, gmx_wallcycle *wcycle)
	Implements LINCS constraining.

static void	gmx::set_lincs_matrix_task (Lincs li, Task li_task, ArrayRef< const real > invmass, int ncc_triangle, int nCrossTaskTriangles)
	Sets the elements in the LINCS matrix for task task.

static void	gmx::set_lincs_matrix (Lincs *li, ArrayRef< const real > invmass, real lambda)
	Sets the elements in the LINCS matrix.

int	gmx::count_triangle_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Counts the number of constraint triangles, i.e. triplets of atoms connected by three constraints. More...

static bool	gmx::more_than_two_sequential_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Finds sequences of sequential constraints.

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.

static void	gmx::lincs_thread_setup (Lincs *li, int natoms)
	Sets up the work division over the threads.

static void	gmx::assign_constraint (Lincs *li, int constraint_index, int a1, int a2, real lenA, real lenB, const ListOfLists< int > &at2con)
	Assign a constraint.

static void	gmx::check_assign_connected (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is connected to other constraints, and if so add those connected constraints to our task.

static void	gmx::check_assign_triangle (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int constraint_index, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is involved in a constraint triangle, and if so add the other two constraints in the triangle to our task.

static void	gmx::set_matrix_indices (Lincs *li, const Task &li_task, const ListOfLists< int > &at2con, bool bSortMatrix)
	Sets matrix indices.

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.

static void	gmx::lincs_warning (gmx_domdec_t dd, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, t_pbc pbc, int ncons, gmx::ArrayRef< const AtomPair > atoms, gmx::ArrayRef< const real > bllen, real wangle, int maxwarn, int *warncount)
	Issues a warning when LINCS constraints cannot be satisfied.

static LincsDeviations	gmx::makeLincsDeviations (const Lincs &lincsd, ArrayRef< const RVec > x, const t_pbc *pbc)
	Determine how well the constraints have been satisfied.

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...

Variables
static const int	gmx::simd_width = 1
	Define simd_width for memory allocation used for SIMD code.

Description

Classes

Functions

Variables