Classes
struct	t_eigvec
	Essential dynamics vector. TODO: split into working data and input data NOTE: called eigvec, because traditionally eigenvectors from PCA analysis were used as essential dynamics vectors, however, vectors used for ED need not have any special properties. More...

struct	t_edvecs
	Essential dynamics vectors per method implementation. More...

struct	t_edflood
	Essential dynamics flooding parameters and work data. TODO: split into working data and input parameters NOTE: The implementation here follows: O.E. Lange, L.V. Schafer, and H. Grubmuller, “Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics,” J. Comp. Chem., 27 1693–1702 (2006) More...

Enumerations
enum	EssentialDynamicsType { EssentialDynamicsType::None, EssentialDynamicsType::EDSampling, EssentialDynamicsType::Flooding }
	Identifies the type of ED: none, normal ED, flooding. More...

enum	EssentialDynamicsStructure { EssentialDynamicsStructure::Reference, EssentialDynamicsStructure::Average, EssentialDynamicsStructure::Origin, EssentialDynamicsStructure::Target }
	Identify on which structure to operate. More...

Functions
std::vector< t_edpar >	read_edi_file (const char *fn, int nr_mdatoms)
	Read in the essential dynamics input file and return its contents. More...

bool	bNeedDoEdsam (const t_edpar &edi)
	Determines whether to perform essential dynamics constraints other than flooding. More...

real	projectx (const t_edpar &edi, rvec xcoll, rvec vec)
	The mass-weighted inner product of two coordinate vectors. Does not subtract average positions, projection on single eigenvector is returned used by: do_linfix, do_linacc, do_radfix, do_radacc, do_radcon Average position is subtracted in ed_apply_constraints prior to calling projectx. More...

void	rad_project (const t_edpar &edi, rvec x, t_eigvec vec)
	Project coordinates onto vector after substracting average position. projection is stored in vec->refproj which is used for radacc, radfix, radcon and center of flooding potential. Average positions are first substracted from x, then added back again. More...

void	project_to_eigvectors (rvec x, t_eigvec vec, const t_edpar &edi)
	Projects coordinates onto eigenvectors and stores result in vec->xproj. Mass-weighting is applied. Subtracts average positions prior to projection and add them afterwards to retain the unchanged vector. More...

real	calc_radius (const t_eigvec &vec)
	Evaluates the distance from reference to current eigenvector projection. More...

void	write_edo_flood (const t_edpar &edi, FILE *fp, real rmsd)
	Output flooding simulation settings and results to file. More...

void	flood_blowup (const t_edpar &edi, rvec *forces_cart)
	Raise forces from subspace into cartesian space. This function lifts the forces from the subspace to the cartesian space all the values not contained in the subspace are assumed to be zero and then a coordinate transformation from eigenvector to cartesian vectors is performed The nonexistent values don't have to be set to zero explicitly, they would occur as zero valued summands, hence we just stop to compute this part of the sum. For every atom we add all the contributions to this atom from all the different eigenvectors. NOTE: one could add directly to the forcefield forces, would mean we wouldn't have to clear the field forces_cart prior the computation, but we compute the forces separately to have them accessible for diagnostics. More...

void	scan_edvec (FILE in, int numAtoms, rvec **vec, int nEig)
	Read eigenvector coordinates for multiple eigenvectors from a file. More...

void	read_edvec (FILE in, int nrAtoms, t_eigvec tvec)
	Read an essential dynamics eigenvector and corresponding step size. More...

bool	readEdVecWithReferenceProjection (FILE in, int nrAtoms, t_eigvec tvec, real initialReferenceProjection, real referenceProjectionSlope)
	Read an essential dynamics eigenvector and intial reference projections and slopes if available. More...

void	setup_edvec (t_eigvec *tvec)
	Allocate working memory for the eigenvectors. More...

void	setup_edi (t_edpar *edi)
	Set up essential dynamics work parameters. More...

bool	ediFileHasConstForceFlooding (int magicNumber)
	Check if edi file version supports CONST_FORCE_FLOODING. More...

bool	ediFileHasValidDataSet (FILE in, int magicNumber)
	Reports reading success of the essential dynamics input file magic number. More...

void	exitWhenMagicNumberIsInvalid (int magicNumber, const char *fn)
	Trigger fatal error if magic number is unsupported. More...

t_edpar	read_edi (FILE in, int nr_mdatoms, bool hasConstForceFlooding, const char fn)
	reads an essential dynamics input file into a essential dynamics data structure. More...

void	do_linfix (rvec *xcoll, const t_edpar &edi, int64_t step)
	Apply fixed linear constraints to essential dynamics variable. More...

void	do_linacc (rvec xcoll, t_edpar edi)
	Apply acceptance linear constraints to essential dynamics variable. More...

void	write_edo (const t_edpar &edi, FILE *fp, real rmsd)
	Write out the projections onto the eigenvectors. The order of output corresponds to ed_output_legend(). More...

Variables
constexpr int	c_oldestUnsupportedMagicNumber = 666
	Oldest (lowest) magic number indicating unsupported essential dynamics input.

constexpr int	c_oldestSupportedMagicNumber = 669
	Oldest (lowest) magic number indicating supported essential dynamics input.

constexpr int	c_latestSupportedMagicNumber = 670
	Latest (highest) magic number indicating supported essential dynamics input.

Enumeration Type Documentation

enum anonymous_namespace{edsam.cpp}::EssentialDynamicsStructure

strong

Identify on which structure to operate.

Enumerator
Reference	Reference structure.
Average	Average Structure.
Origin	Origin Structure.
Target	Target Structure.

enum anonymous_namespace{edsam.cpp}::EssentialDynamicsType

strong

Identifies the type of ED: none, normal ED, flooding.

Enumerator
None	No essential dynamics.
EDSampling	Essential dynamics sampling.
Flooding	Essential dynamics flooding.

Function Documentation

bool anonymous_namespace{edsam.cpp}::bNeedDoEdsam ( const t_edpar & edi )

Determines whether to perform essential dynamics constraints other than flooding.

Parameters

[in] edi the essential dynamics parameters

Returns: true if essential dyanmics constraints need to be performed

real anonymous_namespace{edsam.cpp}::calc_radius ( const t_eigvec & vec )

Evaluates the distance from reference to current eigenvector projection.

Parameters

[in] vec eigenvector

Returns: distance

void anonymous_namespace{edsam.cpp}::do_linacc	(	rvec *	xcoll,
		t_edpar *	edi
	)

Apply acceptance linear constraints to essential dynamics variable.

Parameters

[in,out]	xcoll	The collected coordinates.
[in]	edi	the essential dynamics parameters

void anonymous_namespace{edsam.cpp}::do_linfix	(	rvec *	xcoll,
		const t_edpar &	edi,
		int64_t	step
	)

Apply fixed linear constraints to essential dynamics variable.

Parameters

[in,out]	xcoll	The collected coordinates.
[in]	edi	the essential dynamics parameters
[in]	step	the current simulation step

bool anonymous_namespace{edsam.cpp}::ediFileHasConstForceFlooding ( int magicNumber )

Check if edi file version supports CONST_FORCE_FLOODING.

Parameters

[in] magicNumber indicates the essential dynamics input file version

Returns: true if CONST_FORCE_FLOODING is supported

bool anonymous_namespace{edsam.cpp}::ediFileHasValidDataSet	(	FILE *	in,
		int *	magicNumber
	)

Reports reading success of the essential dynamics input file magic number.

Parameters

[in]	in	pointer to input file
[out]	magicNumber	determines the edi file version

Returns: true if setting file version from input file was successful.

void anonymous_namespace{edsam.cpp}::exitWhenMagicNumberIsInvalid	(	int	magicNumber,
		const char *	fn
	)

Trigger fatal error if magic number is unsupported.

Parameters

[in]	magicNumber	A magic number read from the edi file
[in]	fn	name of input file for error reporting

void anonymous_namespace{edsam.cpp}::flood_blowup	(	const t_edpar &	edi,
		rvec *	forces_cart
	)

Raise forces from subspace into cartesian space. This function lifts the forces from the subspace to the cartesian space all the values not contained in the subspace are assumed to be zero and then a coordinate transformation from eigenvector to cartesian vectors is performed The nonexistent values don't have to be set to zero explicitly, they would occur as zero valued summands, hence we just stop to compute this part of the sum. For every atom we add all the contributions to this atom from all the different eigenvectors. NOTE: one could add directly to the forcefield forces, would mean we wouldn't have to clear the field forces_cart prior the computation, but we compute the forces separately to have them accessible for diagnostics.

Parameters

[in]	edi	Essential dynamics input parameters
[out]	forces_cart	The cartesian forces

void anonymous_namespace{edsam.cpp}::project_to_eigvectors	(	rvec *	x,
		t_eigvec *	vec,
		const t_edpar &	edi
	)

Projects coordinates onto eigenvectors and stores result in vec->xproj. Mass-weighting is applied. Subtracts average positions prior to projection and add them afterwards to retain the unchanged vector.

Parameters

[in]	x	The coordinates to project to an eigenvector
[in,out]	vec	The eigenvectors
[in]	edi	essential dynamics parameters holding average structure and masses

real anonymous_namespace{edsam.cpp}::projectx	(	const t_edpar &	edi,
		rvec *	xcoll,
		rvec *	vec
	)

The mass-weighted inner product of two coordinate vectors. Does not subtract average positions, projection on single eigenvector is returned used by: do_linfix, do_linacc, do_radfix, do_radacc, do_radcon Average position is subtracted in ed_apply_constraints prior to calling projectx.

Parameters

[in]	edi	Essential dynamics parameters
[in]	xcoll	vector of atom coordinates
[in]	vec	vector of coordinates to project onto

Returns: mass-weighted projection.

void anonymous_namespace{edsam.cpp}::rad_project	(	const t_edpar &	edi,
		rvec *	x,
		t_eigvec *	vec
	)

Project coordinates onto vector after substracting average position. projection is stored in vec->refproj which is used for radacc, radfix, radcon and center of flooding potential. Average positions are first substracted from x, then added back again.

Parameters

[in]	edi	essential dynamics parameters with average position
[in]	x	Coordinates to be projected
[out]	vec	eigenvector, radius and refproj are overwritten here

t_edpar anonymous_namespace{edsam.cpp}::read_edi	(	FILE *	in,
		int	nr_mdatoms,
		bool	hasConstForceFlooding,
		const char *	fn
	)

reads an essential dynamics input file into a essential dynamics data structure.

Parameters

[in]	in	input file
[in]	nr_mdatoms	the number of md atoms, used for consistency checking
[in]	hasConstForceFlooding	determines if field "CONST_FORCE_FLOODING" is available in input file
[in]	fn	the file name of the input file for error reporting

Returns: edi essential dynamics parameters

std::vector< t_edpar > anonymous_namespace{edsam.cpp}::read_edi_file	(	const char *	fn,
		int	nr_mdatoms
	)

Read in the essential dynamics input file and return its contents.

Parameters

[in]	fn	the file name of the edi file to be read
[in]	nr_mdatoms	the number of atoms in the simulation

Returns: A vector of containing the essentiail dyanmics parameters. NOTE: edi files may that it may contain several ED data sets from concatenated edi files. The standard case would be a single ED data set, though.

void anonymous_namespace{edsam.cpp}::read_edvec	(	FILE *	in,
		int	nrAtoms,
		t_eigvec *	tvec
	)

Read an essential dynamics eigenvector and corresponding step size.

Parameters

[in]	in	input file
[in]	nrAtoms	number of atoms/coordinates
[out]	tvec	the eigenvector

bool anonymous_namespace{edsam.cpp}::readEdVecWithReferenceProjection	(	FILE *	in,
		int	nrAtoms,
		t_eigvec *	tvec,
		real **	initialReferenceProjection,
		real **	referenceProjectionSlope
	)

Read an essential dynamics eigenvector and intial reference projections and slopes if available.

Eigenvector and its intial reference and slope are stored on the same line in the .edi format. To avoid re-winding the .edi file, the reference eigen-vector and reference data are read in one go.

Parameters

[in]	in	input file
[in]	nrAtoms	number of atoms/coordinates
[out]	tvec	the eigenvector
[out]	initialReferenceProjection	The projection onto eigenvectors as read from file.
[out]	referenceProjectionSlope	The slope of the reference projections.

void anonymous_namespace{edsam.cpp}::scan_edvec	(	FILE *	in,
		int	numAtoms,
		rvec ***	vec,
		int	nEig
	)

Read eigenvector coordinates for multiple eigenvectors from a file.

Parameters

[in]	in	the file to read from
[in]	numAtoms	the number of atoms/coordinates for the eigenvector
[out]	vec	the eigen-vectors
[in]	nEig	the number of eigenvectors

void anonymous_namespace{edsam.cpp}::setup_edi ( t_edpar * edi )

Set up essential dynamics work parameters.

Parameters

[in] edi Essential dynamics working structure.

void anonymous_namespace{edsam.cpp}::setup_edvec ( t_eigvec * tvec )

Allocate working memory for the eigenvectors.

Parameters

[in,out] tvec eigenvector for which memory will be allocated

void anonymous_namespace{edsam.cpp}::write_edo	(	const t_edpar &	edi,
		FILE *	fp,
		real	rmsd
	)

Write out the projections onto the eigenvectors. The order of output corresponds to ed_output_legend().

Parameters

[in]	edi	The essential dyanmics parameters
[in]	fp	The output file
[in]	rmsd	the rmsd to the reference structure

void anonymous_namespace{edsam.cpp}::write_edo_flood	(	const t_edpar &	edi,
		FILE *	fp,
		real	rmsd
	)

Output flooding simulation settings and results to file.

Parameters

[in]	edi	Essential dynamics input parameters
[in]	fp	output file
[in]	rmsd	rmsd to reference structure

Classes

Enumerations

Functions

Variables

Enumeration Type Documentation

Function Documentation