#include <cstdio>
#include <optional>
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/pull_params.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

Include dependency graph for pull.h:

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Description

This file contains datatypes and function declarations necessary for mdrun to interface with the pull code.

Author: Berk Hess

Classes
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...

Functions
const char *	pull_coordinate_units (const t_pull_coord &pcrd)
	Returns the units of the pull coordinate. More...

double	pull_conversion_factor_userinput2internal (const t_pull_coord &pcrd)
	Returns the conversion factor from the pull coord init/rate unit to internal value unit. More...

double	pull_conversion_factor_internal2userinput (const t_pull_coord &pcrd)
	Returns the conversion factor from the pull coord internal value unit to the init/rate unit. More...

double	get_pull_coord_value (pull_t *pull, int coordIndex, const t_pbc &pbc)
	Get the value for pull coord coord_ind. More...

void	register_external_pull_potential (struct pull_t pull, int coord_index, const char provider)
	Registers the provider of an external potential for a coordinate. More...

void	apply_external_pull_coord_force (struct pull_t pull, int coord_index, double coord_force, gmx::ArrayRef< const real > masses, gmx::ForceWithVirial forceWithVirial)
	Apply forces of an external potential to a pull coordinate. More...

void	clear_pull_forces (pull_t *pull)
	Set the all the pull forces to zero. More...

real	pull_potential (pull_t pull, gmx::ArrayRef< const real > masses, const t_pbc &pbc, const t_commrec cr, double t, real lambda, gmx::ArrayRef< const gmx::RVec > x, gmx::ForceWithVirial force, real dvdlambda)
	Determine the COM pull forces and add them to f, return the potential. More...

void	pull_constraint (struct pull_t pull, gmx::ArrayRef< const real > masses, const t_pbc &pbc, const t_commrec cr, double dt, double t, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > xp, gmx::ArrayRef< gmx::RVec > v, tensor vir)
	Constrain the coordinates xp in the directions in x and also constrain v when v != NULL. More...

void	dd_make_local_pull_groups (const t_commrec cr, pull_t pull)
	Make a selection of the home atoms for all pull groups. Should be called at every domain decomposition. More...

struct pull_t *	init_pull (FILE fplog, const pull_params_t pull_params, const t_inputrec ir, const gmx_mtop_t &mtop, const t_commrec cr, gmx::LocalAtomSetManager *atomSets, real lambda)
	Allocate, initialize and return a pull work struct. More...

void	finish_pull (struct pull_t *pull)
	Close the pull output files and delete pull. More...

void	pull_calc_coms (const t_commrec cr, pull_t pull, gmx::ArrayRef< const real > masses, const t_pbc &pbc, double t, gmx::ArrayRef< const gmx::RVec > x, gmx::ArrayRef< gmx::RVec > xp)
	Calculates centers of mass all pull groups. More...

int	pullCheckPbcWithinGroups (const pull_t &pull, gmx::ArrayRef< const gmx::RVec > x, const t_pbc &pbc, real pbcMargin)
	Checks whether all groups that use a reference atom are within PBC restrictions. More...

bool	pullCheckPbcWithinGroup (const pull_t &pull, gmx::ArrayRef< const gmx::RVec > x, const t_pbc &pbc, int groupNr, real pbcMargin)
	Checks whether a specific group that uses a reference atom is within PBC restrictions. More...

bool	pull_have_potential (const pull_t &pull)
	Returns if we have pull coordinates with potential pulling. More...

bool	pull_have_constraint (const pull_t &pull)
	Returns if we have pull coordinates with constraint pulling. More...

bool	pull_have_constraint (const pull_params_t &pullParameters)
	Returns if inputrec has pull coordinates with constraint pulling. More...

real	max_pull_distance2 (const pull_coord_work_t &pcrd, const t_pbc &pbc)
	Returns the maxing distance for pulling. More...

void	updatePrevStepPullCom (pull_t *pull, std::optional< gmx::ArrayRef< double >> comPreviousStep)
	Sets the previous step COM in pull to the current COM, and optionally updates it in the provided ArrayRef. More...

std::vector< double >	prevStepPullCom (const pull_t *pull)
	Returns a copy of the previous step pull COM as flat vector. More...

void	setPrevStepPullCom (pull_t *pull, gmx::ArrayRef< const double > prevStepPullCom)
	Set the previous step pull COM from a flat vector. More...

void	preparePrevStepPullCom (const t_inputrec ir, pull_t pull_work, gmx::ArrayRef< const real > masses, t_state state, const t_state state_global, const t_commrec *cr, bool startingFromCheckpoint)
	Allocates, initializes and communicates the previous step pull COM (if that option is set to true). More...

void	initPullComFromPrevStep (const t_commrec cr, pull_t pull, gmx::ArrayRef< const real > masses, const t_pbc &pbc, gmx::ArrayRef< const gmx::RVec > x)
	Initializes the COM of the previous step (set to initial COM) More...

void	preparePrevStepPullComNewSimulation (const t_commrec cr, pull_t pull_work, gmx::ArrayRef< const real > masses, gmx::ArrayRef< const gmx::RVec > x, const matrix box, PbcType pbcType, std::optional< gmx::ArrayRef< double >> &&comPreviousStep)
	Initializes the previous step pull COM for new simulations (no reading from checkpoint). More...

Variables
static constexpr real	c_pullGroupPbcMargin = 0.9
	Margin for checking pull group PBC distances compared to half the box size.

static constexpr real	c_pullGroupSmallGroupThreshold = 0.5
	Threshold (as a factor of half the box size) for accepting pull groups without explicitly set refatom.

Function Documentation

void apply_external_pull_coord_force	(	struct pull_t *	pull,
		int	coord_index,
		double	coord_force,
		gmx::ArrayRef< const real >	masses,
		gmx::ForceWithVirial *	forceWithVirial
	)

Apply forces of an external potential to a pull coordinate.

This function applies the external scalar force coord_force to the pull coordinate, distributing it over the atoms in the groups involved in the pull coordinate. The corresponding potential energy value should be added to the pull or the module's potential energy term separately by the module itself. This function should be called after pull_potential has been called and, obviously, before the coordinates are updated uses the forces.

Parameters

[in,out]	pull	The pull struct.
[in]	coord_index	The pull coordinate index to set the force for.
[in]	coord_force	The scalar force for the pull coordinate.
[in]	masses	Atoms masses.
[in,out]	forceWithVirial	Force and virial buffers.

void clear_pull_forces ( pull_t * pull )

Set the all the pull forces to zero.

Parameters

pull	The pull group.

void dd_make_local_pull_groups	(	const t_commrec *	cr,
		pull_t *	pull
	)

Make a selection of the home atoms for all pull groups. Should be called at every domain decomposition.

Parameters

cr	Structure for communication info.
pull	The pull group.

void finish_pull ( struct pull_t * pull )

Close the pull output files and delete pull.

Parameters

pull	The pull data structure.

double get_pull_coord_value	(	pull_t *	pull,
		int	coordIndex,
		const t_pbc &	pbc
	)

Get the value for pull coord coord_ind.

Parameters

[in,out]	pull	The pull struct.
[in]	coordIndex	Index of the pull coordinate in the list of coordinates
[in]	pbc	Information structure about periodicity.

Returns: the value of the pull coordinate.

struct pull_t* init_pull	(	FILE *	fplog,
		const pull_params_t *	pull_params,
		const t_inputrec *	ir,
		const gmx_mtop_t &	mtop,
		const t_commrec *	cr,
		gmx::LocalAtomSetManager *	atomSets,
		real	lambda
	)

Allocate, initialize and return a pull work struct.

Parameters

fplog	General output file, normally md.log.
pull_params	The pull input parameters containing all pull settings.
ir	The inputrec.
mtop	The topology of the whole system.
cr	Struct for communication info.
atomSets	The manager that handles the pull atom sets
lambda	FEP lambda.

void initPullComFromPrevStep	(	const t_commrec *	cr,
		pull_t *	pull,
		gmx::ArrayRef< const real >	masses,
		const t_pbc &	pbc,
		gmx::ArrayRef< const gmx::RVec >	x
	)

Initializes the COM of the previous step (set to initial COM)

Parameters

[in]	cr	Struct for communication info.
[in]	pull	The pull data structure.
[in]	masses	Atoms masses.
[in]	pbc	Information struct about periodicity.
[in]	x	The local positions.

real max_pull_distance2	(	const pull_coord_work_t &	pcrd,
		const t_pbc &	pbc
	)

Returns the maxing distance for pulling.

For distance geometries, only dimensions with pcrd->params[dim]=1 are included in the distance calculation. For directional geometries, only dimensions with pcrd->vec[dim]!=0 are included in the distance calculation.

Parameters

[in]	pcrd	Pulling data structure
[in]	pbc	Information on periodic boundary conditions

Returns: The maximume distance

void preparePrevStepPullCom	(	const t_inputrec *	ir,
		pull_t *	pull_work,
		gmx::ArrayRef< const real >	masses,
		t_state *	state,
		const t_state *	state_global,
		const t_commrec *	cr,
		bool	startingFromCheckpoint
	)

Allocates, initializes and communicates the previous step pull COM (if that option is set to true).

If ir->pull->bSetPbcRefToPrevStepCOM is not true nothing is done.

Parameters

[in]	ir	The input options/settings of the simulation.
[in]	pull_work	The COM pull force calculation data structure
[in]	masses	Atoms masses.
[in]	state	The local (to this rank) state.
[in]	state_global	The global state.
[in]	cr	Struct for communication info.
[in]	startingFromCheckpoint	Is the simulation starting from a checkpoint?

void preparePrevStepPullComNewSimulation	(	const t_commrec *	cr,
		pull_t *	pull_work,
		gmx::ArrayRef< const real >	masses,
		gmx::ArrayRef< const gmx::RVec >	x,
		const matrix	box,
		PbcType	pbcType,
		std::optional< gmx::ArrayRef< double >> &&	comPreviousStep
	)

Initializes the previous step pull COM for new simulations (no reading from checkpoint).

Parameters

[in]	cr	Struct for communication info.
[in]	pull_work	The COM pull force calculation data structure.
[in]	masses	Atoms masses.
[in]	x	The local positions.
[in]	box	The current box matrix.
[in]	pbcType	The type of periodic boundary conditions.
[in]	comPreviousStep	The COM of the previous step of each pull group.

std::vector<double> prevStepPullCom ( const pull_t * pull )

Returns a copy of the previous step pull COM as flat vector.

Used for modular simulator checkpointing. Allows to keep the implementation details of pull_t hidden from its users.

Parameters

[in] pull The COM pull force calculation data structure

Returns: A copy of the previous step COM

void pull_calc_coms	(	const t_commrec *	cr,
		pull_t *	pull,
		gmx::ArrayRef< const real >	masses,
		const t_pbc &	pbc,
		double	t,
		gmx::ArrayRef< const gmx::RVec >	x,
		gmx::ArrayRef< gmx::RVec >	xp
	)

Calculates centers of mass all pull groups.

Parameters

[in]	cr	Struct for communication info.
[in]	pull	The pull data structure.
[in]	masses	Atoms masses.
[in]	pbc	Information struct about periodicity.
[in]	t	Time, only used for cylinder ref.
[in]	x	The local positions.
[in,out]	xp	Updated x, can be NULL.

void pull_constraint	(	struct pull_t *	pull,
		gmx::ArrayRef< const real >	masses,
		const t_pbc &	pbc,
		const t_commrec *	cr,
		double	dt,
		double	t,
		gmx::ArrayRef< gmx::RVec >	x,
		gmx::ArrayRef< gmx::RVec >	xp,
		gmx::ArrayRef< gmx::RVec >	v,
		tensor	vir
	)

Constrain the coordinates xp in the directions in x and also constrain v when v != NULL.

Parameters

[in,out]	pull	The pull data.
[in]	masses	Atoms masses.
[in]	pbc	Information struct about periodicity.
[in]	cr	Struct for communication info.
[in]	dt	The time step length.
[in]	t	The time.
[in]	x	Positions.
[in,out]	xp	Updated x, can be NULL.
[in,out]	v	Velocities, which may get a pull correction.
[in,out]	vir	The virial, which, if != NULL, gets a pull correction.

double pull_conversion_factor_internal2userinput ( const t_pull_coord & pcrd )

Returns the conversion factor from the pull coord internal value unit to the init/rate unit.

Parameters

[in] pcrd The pull coordinate to get the conversion factor for.

Returns: the conversion factor.

double pull_conversion_factor_userinput2internal ( const t_pull_coord & pcrd )

Returns the conversion factor from the pull coord init/rate unit to internal value unit.

Parameters

[in] pcrd The pull coordinate to get the conversion factor for.

Returns: the conversion factor.

const char* pull_coordinate_units ( const t_pull_coord & pcrd )

Returns the units of the pull coordinate.

Parameters

[in] pcrd The pull coordinate to query the units for.

Returns: a string with the units of the coordinate.

bool pull_have_constraint ( const pull_t & pull )

Returns if we have pull coordinates with constraint pulling.

Parameters

[in] pull The pull data structure.

bool pull_have_constraint ( const pull_params_t & pullParameters )

Returns if inputrec has pull coordinates with constraint pulling.

Parameters

[in] pullParameters Pulling input parameters from input record.

bool pull_have_potential ( const pull_t & pull )

Returns if we have pull coordinates with potential pulling.

Parameters

[in] pull The pull data structure.

real pull_potential	(	pull_t *	pull,
		gmx::ArrayRef< const real >	masses,
		const t_pbc &	pbc,
		const t_commrec *	cr,
		double	t,
		real	lambda,
		gmx::ArrayRef< const gmx::RVec >	x,
		gmx::ForceWithVirial *	force,
		real *	dvdlambda
	)

Determine the COM pull forces and add them to f, return the potential.

Parameters

[in,out]	pull	The pull struct.
[in]	masses	Atoms masses.
[in]	pbc	Information struct about periodicity.
[in]	cr	Struct for communication info.
[in]	t	Time.
[in]	lambda	The value of lambda in FEP calculations.
[in]	x	Positions.
[in,out]	force	Forces and virial.
[out]	dvdlambda	Pull contribution to dV/d(lambda).

Returns: The pull potential energy.

bool pullCheckPbcWithinGroup	(	const pull_t &	pull,
		gmx::ArrayRef< const gmx::RVec >	x,
		const t_pbc &	pbc,
		int	groupNr,
		real	pbcMargin
	)

Checks whether a specific group that uses a reference atom is within PBC restrictions.

Groups that use a reference atom for determining PBC should have all their atoms within half the box size from the PBC atom. The box size is used per dimension for rectangular boxes, but can be a combination of dimensions for triclinic boxes, depending on which dimensions are involved in the pull coordinates a group is involved in. A margin is specified to ensure that atoms are not too close to the maximum distance. Only one group is checked.

Should be called without MPI parallelization and after pull_calc_coms() has been called at least once.

Parameters

[in]	pull	The pull data structure
[in]	x	The coordinates
[in]	pbc	Information struct about periodicity
[in]	groupNr	The index of the group (in pull.group[]) to check
[in]	pbcMargin	The minimum margin (as a fraction) to half the box size

Returns: true if the group obeys PBC otherwise false

int pullCheckPbcWithinGroups	(	const pull_t &	pull,
		gmx::ArrayRef< const gmx::RVec >	x,
		const t_pbc &	pbc,
		real	pbcMargin
	)

Checks whether all groups that use a reference atom are within PBC restrictions.

Groups that use a reference atom for determining PBC should have all their atoms within half the box size from the PBC atom. The box size is used per dimension for rectangular boxes, but can be a combination of dimensions for triclinic boxes, depending on which dimensions are involved in the pull coordinates a group is involved in. A margin is specified to ensure that atoms are not too close to the maximum distance.

Should be called without MPI parallelization and after pull_calc_coms() has been called at least once.

Parameters

[in]	pull	The pull data structure
[in]	x	The coordinates
[in]	pbc	Information struct about periodicity
[in]	pbcMargin	The minimum margin (as a fraction) to half the box size

Returns: -1 when all groups obey PBC or the first group index that fails PBC

void register_external_pull_potential	(	struct pull_t *	pull,
		int	coord_index,
		const char *	provider
	)

Registers the provider of an external potential for a coordinate.

This function is only used for checking the consistency of the pull setup. For each pull coordinate of type external-potential, selected by the user in the mdp file, there has to be a module that provides this potential. The module registers itself as the provider by calling this function. The passed provider string has to match the string that the user passed with the potential-provider pull coordinate mdp option. This function should be called after init_pull has been called and before pull_potential is called for the first time. This function does many consistency checks and when it returns and the first call to do_potential passes, the pull setup is guaranteed to be correct (unless the module doesn't call apply_external_pull_coord_force every step or calls it with incorrect forces). This registering function will exit with a (release) assertion failure when used incorrely or with a fatal error when the user (mdp) input in inconsistent.

Thread-safe for simultaneous registration from multiple threads.

Parameters

[in,out]	pull	The pull struct.
[in]	coord_index	The pull coordinate index to register the external potential for.
[in]	provider	Provider string, should match the potential-provider pull coordinate mdp option.

void setPrevStepPullCom	(	pull_t *	pull,
		gmx::ArrayRef< const double >	prevStepPullCom
	)

Set the previous step pull COM from a flat vector.

Used to restore modular simulator checkpoints. Allows to keep the implementation details of pull_t hidden from its users.

Parameters

[in]	pull	The COM pull force calculation data structure
[in]	prevStepPullCom	The previous step COM to set

void updatePrevStepPullCom	(	pull_t *	pull,
		std::optional< gmx::ArrayRef< double >>	comPreviousStep
	)

Sets the previous step COM in pull to the current COM, and optionally updates it in the provided ArrayRef.

Parameters

[in]	pull	The COM pull force calculation data structure
[in]	comPreviousStep	The COM of the previous step of each pull group

Description

Classes

Functions

Variables

Function Documentation