#include "gmxpre.h"
#include "poscalc.h"
#include <cstring>
#include <algorithm>
#include <vector>
#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "centerofmass.h"
#include "position.h"

Include dependency graph for poscalc.cpp:

Description

Implements gmx::PositionCalculationCollection and functions in poscalc.h.

Todo:: There is probably some room for optimization in the calculation of positions with bases. In particular, the current implementation may do a lot of unnecessary copying. The interface would need to be changed to make it possible to use the same output positions for several calculations.

Todo:: The current algorithm for setting up base calculations could be improved in cases when there are calculations that cannot use a common base but still overlap partially (e.g., with three calculations A, B, and C such that A could use both B and C as a base, but B and C cannot use the same base). Setting up the bases in an optimal manner in every possible situation can be quite difficult unless several bases are allowed for one calculation, but better heuristics could probably be implemented. For best results, the setup should probably be postponed (at least partially) to gmx_ana_poscalc_init_eval().

Author: Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
class	gmx::PositionCalculationCollection::Impl
	Private implementation class for PositionCalculationCollection. More...

struct	gmx_ana_poscalc_t
	Data structure for position calculation. More...

Functions
static e_index_t	index_type_for_poscalc (e_poscalc_t type)
	Returns the partition type for a given position type. More...

PositionCalculationCollection::RequiredTopologyInfo	gmx::anonymous_namespace{poscalc.cpp}::requiredTopologyInfo (e_poscalc_t type, int flags)
	Helper function for determining required topology information.

static void	set_poscalc_maxindex (gmx_ana_poscalc_t pc, gmx_ana_index_t g, bool bBase)
	Initializes position calculation using the maximum possible input index. More...

static bool	can_use_base (gmx_ana_poscalc_t *pc)
	Checks whether a position calculation should use a base at all. More...

static bool	should_merge (gmx_ana_poscalc_t pc1, gmx_ana_poscalc_t pc2, gmx_ana_index_t g1, gmx_ana_index_t g)
	Checks whether two position calculations should use a common base. More...

static gmx_ana_poscalc_t *	create_simple_base (gmx_ana_poscalc_t *pc)
	Creates a static base for position calculation. More...

static void	merge_to_base (gmx_ana_poscalc_t base, gmx_ana_poscalc_t pc)
	Merges a calculation into another calculation such that the new calculation can be used as a base. More...

static void	merge_bases (gmx_ana_poscalc_t tbase, gmx_ana_poscalc_t mbase)
	Merges two bases into one. More...

static void	setup_base (gmx_ana_poscalc_t *pc)
	Setups the static base calculation for a position calculation. More...

void	gmx_ana_poscalc_set_flags (gmx_ana_poscalc_t *pc, int flags)
	Sets the flags for position calculation. More...

void	gmx_ana_poscalc_set_maxindex (gmx_ana_poscalc_t pc, gmx_ana_index_t g)
	Sets the maximum possible input index group for position calculation. More...

void	gmx_ana_poscalc_init_pos (gmx_ana_poscalc_t pc, gmx_ana_pos_t p)
	Initializes positions for position calculation output. More...

void	gmx_ana_poscalc_free (gmx_ana_poscalc_t *pc)
	Frees the memory allocated for position calculation. More...

gmx::PositionCalculationCollection::RequiredTopologyInfo	gmx_ana_poscalc_required_topology_info (gmx_ana_poscalc_t *pc)
	Returns true if the position calculation requires topology information. More...

void	gmx_ana_poscalc_update (gmx_ana_poscalc_t pc, gmx_ana_pos_t p, gmx_ana_index_t g, t_trxframe fr, const t_pbc *pbc)
	Updates a single COM/COG structure for a frame. More...

Function Documentation

static bool can_use_base ( gmx_ana_poscalc_t * pc )

static

Checks whether a position calculation should use a base at all.

Parameters

[in] pc Position calculation data to check.

Returns: true if pc can use a base and gets some benefit out of it, false otherwise.

static gmx_ana_poscalc_t* create_simple_base ( gmx_ana_poscalc_t * pc )

static

Creates a static base for position calculation.

Parameters

pc	Data structure to copy.

Returns: Pointer to a newly allocated base for pc.

Creates and returns a deep copy of pc, but clears the POS_DYNAMIC and POS_MASKONLY flags. The newly created structure is set as the base (gmx_ana_poscalc_t::sbase) of pc and inserted in the collection before pc.

void gmx_ana_poscalc_free ( gmx_ana_poscalc_t * pc )

Frees the memory allocated for position calculation.

Parameters

pc	Position calculation data to be freed.

The pc pointer is invalid after the call.

void gmx_ana_poscalc_init_pos	(	gmx_ana_poscalc_t *	pc,
		gmx_ana_pos_t *	p
	)

Initializes positions for position calculation output.

Parameters

[in]	pc	Position calculation data structure.
[out]	p	Output positions.

Calls to gmx_ana_poscalc_update() using pc should use only positions initialized with this function. The p->g pointer is initialized to point to an internal group that contains the maximum index group set with gmx_ana_poscalc_set_maxindex().

gmx::PositionCalculationCollection::RequiredTopologyInfo gmx_ana_poscalc_required_topology_info ( gmx_ana_poscalc_t * pc )

Returns true if the position calculation requires topology information.

Parameters

[in] pc Position calculation data to query.

Returns: Which topology information pc requires for initialization and/or evaluation.

void gmx_ana_poscalc_set_flags	(	gmx_ana_poscalc_t *	pc,
		int	flags
	)

Sets the flags for position calculation.

Parameters

[in,out]	pc	Position calculation data structure.
[in]	flags	New flags.

flags are added to the old flags. If calculation type is POS_ATOM, POS_MASS is automatically cleared. If both POS_DYNAMIC and POS_MASKONLY are provided, POS_DYNAMIC is cleared. If calculation type is not POS_RES or POS_MOL, POS_COMPLMAX and POS_COMPLWHOLE are automatically cleared.

void gmx_ana_poscalc_set_maxindex	(	gmx_ana_poscalc_t *	pc,
		gmx_ana_index_t *	g
	)

Sets the maximum possible input index group for position calculation.

Parameters

[in,out]	pc	Position calculation data structure.
[in]	g	Maximum index group for the calculation.

Subsequent calls to gmx_ana_poscalc_update() should use only subsets of g for evaluation.

The topology should have been set for the collection of which pc is a member.

void gmx_ana_poscalc_update	(	gmx_ana_poscalc_t *	pc,
		gmx_ana_pos_t *	p,
		gmx_ana_index_t *	g,
		t_trxframe *	fr,
		const t_pbc *	pbc
	)

Updates a single COM/COG structure for a frame.

Parameters

[in]	pc	Position calculation data.
[in,out]	p	Output positions, initialized previously with gmx_ana_poscalc_init_pos() using `pc`.
[in]	g	Index group to use for the update.
[in]	fr	Current frame.
[in]	pbc	PBC data, or NULL if no PBC should be used.

gmx_ana_poscalc_init_frame() should be called for each frame before calling this function.

static e_index_t index_type_for_poscalc ( e_poscalc_t type )

static

Returns the partition type for a given position type.

Parameters

[in] type e_poscalc_t value to convert.

Returns: Corresponding e_indet_t.

static void merge_bases	(	gmx_ana_poscalc_t *	tbase,
		gmx_ana_poscalc_t *	mbase
	)

static

Merges two bases into one.

Parameters

[in,out]	tbase	Base calculation to merge to.
[in]	mbase	Base calculation to merge to `tbase`.

After the call, mbase has been freed and tbase is used as the base for all calculations that previously had mbase as their base. It is assumed that any overlap between tbase and mbase is in complete blocks, i.e., that the merge is possible.

static void merge_to_base	(	gmx_ana_poscalc_t *	base,
		gmx_ana_poscalc_t *	pc
	)

static

Merges a calculation into another calculation such that the new calculation can be used as a base.

Parameters

[in,out]	base	Base calculation to merge to.
[in,out]	pc	Position calculation to merge to `base`.

After the call, base can be used as a base for pc (or any calculation that used it as a base). It is assumed that any overlap between base and pc is in complete blocks, i.e., that the merge is possible.

static void set_poscalc_maxindex	(	gmx_ana_poscalc_t *	pc,
		gmx_ana_index_t *	g,
		bool	bBase
	)

static

Initializes position calculation using the maximum possible input index.

Parameters

[in,out]	pc	Position calculation data structure.
[in]	g	Maximum index group for the calculation.
[in]	bBase	Whether `pc` will be used as a base or not.

bBase affects on how the pc->gmax field is initialized.

static void setup_base ( gmx_ana_poscalc_t * pc )

static

Setups the static base calculation for a position calculation.

Parameters

[in,out] pc Position calculation to setup the base for.

static bool should_merge	(	gmx_ana_poscalc_t *	pc1,
		gmx_ana_poscalc_t *	pc2,
		gmx_ana_index_t *	g1,
		gmx_ana_index_t *	g
	)

static

Checks whether two position calculations should use a common base.

Parameters

[in]	pc1	Calculation 1 to check for.
[in]	pc2	Calculation 2 to check for.
[in]	g1	Index group structure that contains the atoms from `pc1`.
[in,out]	g	Working space, should have enough allocated memory to contain the intersection of the atoms in `pc1` and `pc2`.

Returns: true if the two calculations should be merged to use a common base, false otherwise.

Description

Classes

Functions

Function Documentation