Store the information of a group of atoms in a structure-of-arrays (SoA) style. More...

#include <colvaratoms.h>

Inheritance diagram for cvm::atom_group:

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Collaboration diagram for cvm::atom_group:

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Classes
class	atom_modifier
	The temporary AoS interface to modify `cvm::atom_group`. More...

class	group_force_object
	A helper class for applying forces on an atom group in a way that is aware of the fitting group. NOTE: you are encouraged to use get_group_force_object() to get an instance of group_force_object instead of constructing directly. More...

struct	simple_atom
	A simplified class of `cvm::atom` that can be used with `cvm::atom_group::atom_modifier`. More...

Public Member Functions
	atom_group ()
	Default constructor. More...

	atom_group (char const *key_in)
	Create a group object, assign a name to it.

	~atom_group () override
	Destructor. More...

int	init ()
	Set default values for common flags.

int	setup ()
	Update data required to calculate cvc's. More...

int	init_dependencies () override
	Initialize dependency tree. More...

const std::vector< feature * > &	features () const override
	Implementation of the feature list accessor for atom group. More...

std::vector< feature * > &	modify_features () override

atom_modifier	get_atom_modifier ()
	Get the atom modifier object associated with this SoA atom group. More...

void	clear_soa ()
	Remove all atoms from this SoA group and the proxy. More...

int	parse (std::string const &conf)
	Initialize the group by looking up its configuration.

int	parse_fitting_options (std::string const &group_conf)
	Initialize the fitting group by looking up its configuration.

int	set_dummy ()
	Set this group as a dummy group (no actual atoms)

int	set_dummy_pos (cvm::atom_pos const &pos)
	If this group is dummy, set the corresponding position.

void	update_total_mass ()
	Update the total mass of the atom group.

void	update_total_charge ()
	Update the total mass of the group.

void	print_properties (std::string const &colvar_name, int i, int j)
	Print the updated the total mass and charge of a group. More...

std::vector< int > const &	ids () const
	Internal atom IDs (populated during initialization)

std::string const	print_atom_ids () const

int	create_sorted_ids ()
	Allocates and populates sorted_ids and sorted_ids_map.

std::vector< int > const &	sorted_ids () const
	Sorted internal atom IDs (populated on-demand by create_sorted_ids);. More...

std::vector< int > const &	sorted_ids_map () const
	Map entries of sorted_atoms_ids onto the original positions in the group.

void	read_positions ()
	Get the current positions.

void	calc_apply_roto_translation ()
	(Re)calculate the optimal roto-translation

void	setup_rotation_derivative ()
	Setup the `rot_deriv` object for the calculation of derivative of the optimal roto-translation.

void	center_ref_pos ()
	Save aside the center of geometry of the reference positions, then subtract it from them. More...

void	rotate (const cvm::rmatrix &rot_mat)
	Rotate all atoms by a rotation matrix.

void	apply_translation (cvm::rvector const &t)
	Move all positions.

void	read_velocities ()
	Get the current velocities. More...

void	read_total_forces ()
	Get the current total_forces. More...

int	calc_required_properties ()
	Recompute all mutable quantities that are required to compute CVCs.

int	calc_center_of_geometry ()
	Calculate the center of geometry of the atomic positions, assuming that they are already pbc-wrapped.

std::vector< cvm::real >	positions () const
	Return a copy of the current atom positions.

cvm::atom_pos	center_of_geometry () const
	Return the center of geometry of the atomic positions.

int	calc_center_of_mass ()
	Calculate the center of mass of the atomic positions, assuming that they are already pbc-wrapped.

cvm::atom_pos	center_of_mass () const
	Return the center of mass (COM) of the atomic positions.

cvm::rvector	center_of_mass_scalar_gradient () const
	Return previously gradient of scalar variable with respect to the COM.

std::vector< cvm::real >	positions_shifted (cvm::rvector const &shift) const
	Return a copy of the current atom positions, shifted by a constant vector.

std::vector< cvm::real >	velocities () const
	Return a copy of the current atom velocities.

int	calc_dipole (cvm::atom_pos const &dipole_center)
	Calculate the dipole of the atom group around the specified center.

cvm::rvector	dipole () const
	Return the (previously calculated) dipole of the atom group.

std::vector< cvm::real >	total_forces () const
	Return a copy of the total forces.

cvm::rvector	total_force () const
	Return a copy of the aggregated total force on the group.

void	set_weighted_gradient (cvm::rvector const &grad)
	Shorthand: save the specified gradient on each atom, weighting with the atom mass (mostly used in combination with `cvm::atom_group::center_of_mass()` )

void	calc_fit_gradients ()
	Calculate the derivatives of the fitting transformation.

template<bool B_ag_center, bool B_ag_rotate, typename main_force_accessor_T , typename fitting_force_accessor_T >
void	calc_fit_forces_impl (main_force_accessor_T accessor_main, fitting_force_accessor_T accessor_fitting) const
	Actual implementation of `calc_fit_gradients` and `calc_fit_forces`. The template is used to avoid branching inside the loops in case that the CPU branch prediction is broken (or further migration to GPU code). More...

template<typename main_force_accessor_T , typename fitting_force_accessor_T >
void	calc_fit_forces (main_force_accessor_T accessor_main, fitting_force_accessor_T accessor_fitting) const
	Calculate or apply the fitting group forces from the main group forces. More...

void	apply_colvar_force (cvm::real const &force)
	Used by a (scalar) colvar to apply its force on its atom_group members. More...

void	apply_force (cvm::rvector const &force)
	Apply a force "to the center of mass", i.e. the force is distributed on each atom according to its mass. More...

void	do_feature_side_effects (int id) override

size_t	size () const
	Return the number of atoms of this group.

void	reset_atoms_data ()
	Clear the atom positions, velocities, gradients and total forces.

void	set_ref_pos_from_aos (const std::vector< cvm::atom_pos > &pos_aos)
	Setup reference positions from AOS.

simple_atom	operator[] (size_t i) const
	Read-only operator[].

group_force_object	get_group_force_object ()

Accessors to atom IDs
int &	id (size_t i)

const int &	id (size_t i) const

Accessors to positions
cvm::real &	pos_x (size_t i)

cvm::real &	pos_y (size_t i)

cvm::real &	pos_z (size_t i)

const cvm::real &	pos_x (size_t i) const

const cvm::real &	pos_y (size_t i) const

const cvm::real &	pos_z (size_t i) const

Accessors to velocities
cvm::real &	vel_x (size_t i)

cvm::real &	vel_y (size_t i)

cvm::real &	vel_z (size_t i)

const cvm::real &	vel_x (size_t i) const

const cvm::real &	vel_y (size_t i) const

const cvm::real &	vel_z (size_t i) const

Accessors to gradients
cvm::real &	grad_x (size_t i)

cvm::real &	grad_y (size_t i)

cvm::real &	grad_z (size_t i)

const cvm::real &	grad_x (size_t i) const

const cvm::real &	grad_y (size_t i) const

const cvm::real &	grad_z (size_t i) const

Accessors to total forces
cvm::real &	total_force_x (size_t i)

cvm::real &	total_force_y (size_t i)

cvm::real &	total_force_z (size_t i)

const cvm::real &	total_force_x (size_t i) const

const cvm::real &	total_force_y (size_t i) const

const cvm::real &	total_force_z (size_t i) const

Accessors to reference positions
cvm::real &	ref_pos_x (size_t i)

cvm::real &	ref_pos_y (size_t i)

cvm::real &	ref_pos_z (size_t i)

const cvm::real &	ref_pos_x (size_t i) const

const cvm::real &	ref_pos_y (size_t i) const

const cvm::real &	ref_pos_z (size_t i) const

Accessors to positions before rotation
cvm::real &	pos_unrotated_x (size_t i)

cvm::real &	pos_unrotated_y (size_t i)

cvm::real &	pos_unrotated_z (size_t i)

const cvm::real &	pos_unrotated_x (size_t i) const

const cvm::real &	pos_unrotated_y (size_t i) const

const cvm::real &	pos_unrotated_z (size_t i) const

Accessors to masses
cvm::real &	mass (size_t i)

const cvm::real &	mass (size_t i) const

Accessors to weights
cvm::real &	weight (size_t i)

const cvm::real &	weight (size_t i) const

Accessors to charges
cvm::real &	charge (size_t i)

const cvm::real &	charge (size_t i) const

Accessors to fit gradients
cvm::real &	fit_gradients_x (size_t i)

cvm::real &	fit_gradients_y (size_t i)

cvm::real &	fit_gradients_z (size_t i)

const cvm::real &	fit_gradients_x (size_t i) const

const cvm::real &	fit_gradients_y (size_t i) const

const cvm::real &	fit_gradients_z (size_t i) const

Accessors to group forces
cvm::real &	group_forces_x (size_t i)

cvm::real &	group_forces_y (size_t i)

cvm::real &	group_forces_z (size_t i)

const cvm::real &	group_forces_x (size_t i) const

const cvm::real &	group_forces_y (size_t i) const

const cvm::real &	group_forces_z (size_t i) const

Public Member Functions inherited from colvarparse
	colvarparse ()
	Default constructor.

	colvarparse (const std::string &conf)
	Constructor that stores the object's config string.

void	clear ()
	Set the object ready to parse a new configuration string.

void	set_string (std::string const &conf)
	Set a new config string for this object.

	~colvarparse () override
	Default destructor.

std::string const &	get_config () const
	Get the configuration string (includes comments)

int	check_keywords (std::string &conf, char const *key)
	Check that all the keywords within "conf" are in the list of allowed keywords; this will invoke strip_values() first and then loop over all words.

void	clear_keyword_registry ()
	Use this after parsing a config string (note that check_keywords() calls it already)

bool	get_keyval (std::string const &conf, char const *key, int &value, int const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, size_t &value, size_t const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::step_number &value, cvm::step_number const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::string &value, std::string const &def_value=std::string(""), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::real &value, cvm::real const &def_value=0.0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::rvector &value, cvm::rvector const &def_value=cvm::rvector(), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::quaternion &value, cvm::quaternion const &def_value=cvm::quaternion(), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, colvarvalue &value, colvarvalue const &def_value=colvarvalue(colvarvalue::type_notset), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< int > &values, std::vector< int > const &def_values=std::vector< int >(0, 0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< size_t > &values, std::vector< size_t > const &def_values=std::vector< size_t >(0, 0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< long > &values, std::vector< long > const &def_values=std::vector< long >(0, 0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< std::string > &values, std::vector< std::string > const &def_values=std::vector< std::string >(0, std::string("")), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::real > &values, std::vector< cvm::real > const &def_values=std::vector< cvm::real >(0, 0.0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::rvector > &values, std::vector< cvm::rvector > const &def_values=std::vector< cvm::rvector >(0, cvm::rvector()), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::quaternion > &values, std::vector< cvm::quaternion > const &def_values=std::vector< cvm::quaternion >(0, cvm::quaternion()), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< colvarvalue > &values, std::vector< colvarvalue > const &def_values=std::vector< colvarvalue >(0, colvarvalue(colvarvalue::type_notset)), Parse_Mode const parse_mode=parse_normal)

bool	key_lookup (std::string const &conf, char const key, std::string data=nullptr, size_t *save_pos=nullptr)
	Low-level function for parsing configuration strings; automatically adds the requested keyword to the list of valid ones. More...

std::istream &	read_config_line (std::istream &is, std::string &line)
	Reads a configuration line, adds it to config_string, and returns the stream. More...

template<>
int	_get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, bool &value, bool const &)

template<>
int	_get_keyval_scalar_novalue_ (std::string const &key_str, bool &value, Parse_Mode const &parse_mode)

Public Member Functions inherited from colvarparams
int	param_exists (std::string const &param_name)
	Whether the parameter param_name exists.

virtual std::vector< std::string >	get_param_names ()
	Get a copy of the names of registered parameters.

virtual std::vector< std::string >	get_param_grad_names ()
	Get a copy of the names of registered parameter gradients.

virtual void const *	get_param_ptr (std::string const &param_name)
	Pointer to the parameter param_name.

virtual void const *	get_param_grad_ptr (std::string const &param_name)
	Pointer to the gradient of parameter param_name.

virtual cvm::real	get_param (std::string const &param_name)
	Value of the parameter param_name (must be a scalar)

virtual int	set_param (std::string const &param_name, void const *new_value)
	Set the named parameter to the given value. More...

Public Member Functions inherited from colvardeps
int	get_time_step_factor () const
	returns time_step_factor

void	init_feature (int feature_id, const char *description, feature_type type)
	Pair a numerical feature ID with a description and type.

bool	is_not_set (int id)

bool	is_dynamic (int id)

bool	is_static (int id)

bool	is_user (int id)

virtual const std::vector< feature * > &	features () const =0

virtual std::vector< feature * > &	modify_features ()=0

void	add_child (colvardeps *child)

void	remove_child (colvardeps *child)

void	remove_all_children ()

bool	is_enabled (int f=f_cv_active) const

bool	is_available (int f=f_cv_active) const

void	provide (int feature_id, bool truefalse=true)

void	set_enabled (int feature_id, bool truefalse=true)
	Enable or disable, depending on flag value.

int	enable (int f, bool dry_run=false, bool toplevel=true, bool error=false)

int	disable (int f)

void	free_children_deps ()

void	restore_children_deps ()
	re-enable children features (to be used when object becomes active)

int	decr_ref_count (int f)

virtual void	do_feature_side_effects (int)

virtual int	init_dependencies ()=0
	Initialize dependency tree for object of a derived class. More...

void	require_feature_self (int f, int g)
	Make feature f require feature g within the same object.

void	exclude_feature_self (int f, int g)
	Make features f and g mutually exclusive within the same object.

void	require_feature_children (int f, int g)
	Make feature f require feature g within children.

void	require_feature_alt (int f, int g, int h)
	Make feature f require either g or h within the same object.

void	require_feature_alt (int f, int g, int h, int i)
	Make feature f require any of g, h, or i within the same object.

void	require_feature_alt (int f, int g, int h, int i, int j)
	Make feature f require any of g, h, i, or j within the same object.

void	print_state ()
	print all enabled features and those of children, for debugging

void	check_enabled (int f, std::string const &reason) const
	Check that a feature is enabled, raising COLVARS_BUG_ERROR if not.

Static Public Member Functions
static std::vector< cvm::real >	pos_aos_to_soa (const std::vector< cvm::atom_pos > &aos_in)
	A helper function to re-arrange the a vector of cvm::atom_pos (in AoS style xyz...xyz) to an SoA vector (x...xy...yz...z)

static void	delete_features ()

static simple_atom	init_atom_from_proxy (colvarproxy *const p, cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id)
	Initialize an instance of `cvm::atom_group::simple_atom` from `colvarproxy`. More...

static simple_atom	init_atom_from_proxy (colvarproxy *const p, int atom_number)
	Initialize an instance of `cvm::atom_group::simple_atom` from `colvarproxy`. More...

static simple_atom	init_atom_from_proxy (colvarproxy *const p, const simple_atom &atom)
	Initialize an instance of `cvm::atom_group::simple_atom` from `colvarproxy`. More...

static int	overlap (const atom_group &g1, const atom_group &g2)
	Detect whether two groups share atoms. More...

Static Public Member Functions inherited from colvarparse
static std::string	to_lower_cppstr (std::string const &in)
	Return a lowercased copy of the string.

static std::istream &	getline_nocomments (std::istream &is, std::string &s)
	Works as std::getline() but also removes everything between a comment character and the following newline.

static int	check_braces (std::string const &conf, size_t const start_pos)
	Check if the content of a config string has matching braces. More...

static int	check_ascii (std::string const &conf)
	Check that a config string contains non-ASCII characters. More...

static void	split_string (const std::string &data, const std::string &delim, std::vector< std::string > &dest)
	Split a string with a specified delimiter into a vector. More...

Public Attributes
std::string	name
	Optional name to reuse properties of this in other groups.

bool	b_dummy
	If this option is on, this group merely acts as a wrapper for a fixed position; any calls to atoms within or to functions that return disaggregated data will fail.

std::string	key
	Keyword used to define the group.

cvm::atom_group *	fitting_group
	If f_ag_center or f_ag_rotate is true, use this group to define the transformation (default: this group itself)

cvm::rotation	rot
	The rotation calculated automatically if f_ag_rotate is defined.

bool	noforce
	Don't apply any force on this group (use its coordinates only to calculate a colvar)

bool	b_user_defined_fit
	Indicates that the user has explicitly set centerToReference or rotateReference, and the corresponding reference: cvc's (eg rmsd, eigenvector) will not override the user's choice.

std::vector< cvm::real >	fit_gradients
	Derivatives of the fitting transformation.

cvm::real	total_mass
	Total mass of the atom group.

cvm::real	total_charge
	Total charge of the atom group.

rotation_derivative *	rot_deriv
	Rotation derivative;.

Public Attributes inherited from colvardeps
std::string	description

Static Public Attributes
static std::vector< feature * >	ag_features
	Implementation of the feature list for atom group.

Static Public Attributes inherited from colvarparse
static const char *const	white_space = " \t"
	Accepted white space delimiters, used in key_lookup()

Private Attributes
size_t	num_atoms
	Number of atoms.

std::vector< int >	atoms_index
	SOA atom indices (size: num_atoms)

std::vector< cvm::real >	atoms_pos
	SOA atom positions (size: 3 * num_atoms)

std::vector< cvm::real >	atoms_charge
	SOA atom charges (size: num_atoms)

std::vector< cvm::real >	atoms_vel
	SOA atom velocities (size: 3 * num_atoms)

std::vector< cvm::real >	atoms_mass
	SOA atom mass (size: num_atoms)

std::vector< cvm::real >	atoms_grad
	SOA atom gradients (size: 3 * num_atoms)

std::vector< cvm::real >	atoms_total_force
	SOA atom total forces (size: 3 * num_atoms)

std::vector< cvm::real >	atoms_weight
	Atom masses divided by total mass (size: num_atoms)

std::vector< int >	atoms_ids
	Internal atom IDs for host code.

std::vector< int >	sorted_atoms_ids
	Sorted list of internal atom IDs (populated on-demand by create_sorted_ids); used to read coordinate files.

std::vector< int >	sorted_atoms_ids_map
	Map entries of sorted_atoms_ids onto the original positions in the group.

cvm::atom_pos	dummy_atom_pos
	Dummy atom position.

int	index
	Index in the colvarproxy arrays (if the group is scalable)

std::vector< cvm::real >	group_forces
	The temporary forces acting on the main group atoms. Currently this is only used for calculating the fitting group forces for non-scalar components.

std::vector< cvm::real >	ref_pos
	use reference coordinates for f_ag_center or f_ag_rotate

size_t	num_ref_pos

cvm::atom_pos	ref_pos_cog
	Center of geometry of the reference coordinates; regardless of whether f_ag_center is true, ref_pos is centered to zero at initialization, and ref_pos_cog serves to center the positions.

cvm::atom_pos	cog
	Center of geometry.

cvm::atom_pos	cog_orig
	Center of geometry before any fitting.

std::vector< cvm::real >	atoms_pos_unrotated
	Unrotated atom positions for fit gradients.

cvm::atom_pos	com
	Center of mass.

cvm::rvector	scalar_com_gradient
	The derivative of a scalar variable with respect to the COM.

cvm::rvector	dip
	Dipole moment of the atom group.

std::mutex	modify_lock
	Lock for modifier.

Additional Inherited Members
Public Types inherited from colvarparse
enum	Parse_Mode { parse_null = 0 , parse_echo = (1<<1) , parse_echo_default = (1<<2) , parse_deprecation_warning = (1<<3) , parse_silent = 0 , parse_required = (1<<16) , parse_override = (1<<17) , parse_restart = (1<<18) , parse_normal = (1<<1) \| (1<<2) \| (1<<17) , parse_deprecated = (1<<1) \| (1<<3) \| (1<<17) }
	How a keyword is parsed in a string. More...

Public Types inherited from colvardeps
enum	features_biases { f_cvb_active , f_cvb_awake , f_cvb_step_zero_data , f_cvb_apply_force , f_cvb_bypass_ext_lagrangian , f_cvb_get_total_force , f_cvb_output_acc_work , f_cvb_history_dependent , f_cvb_time_dependent , f_cvb_scalar_variables , f_cvb_calc_pmf , f_cvb_calc_ti_samples , f_cvb_write_ti_samples , f_cvb_write_ti_pmf , f_cvb_scale_biasing_force , f_cvb_extended , f_cvb_smp , f_cvb_ntot }

enum	features_colvar { f_cv_active , f_cv_awake , f_cv_apply_force , f_cv_gradient , f_cv_collect_gradient , f_cv_collect_atom_ids , f_cv_fdiff_velocity , f_cv_total_force , f_cv_total_force_calc , f_cv_total_force_current_step , f_cv_subtract_applied_force , f_cv_Jacobian , f_cv_hide_Jacobian , f_cv_extended_Lagrangian , f_cv_external , f_cv_Langevin , f_cv_output_energy , f_cv_output_value , f_cv_output_velocity , f_cv_output_applied_force , f_cv_output_total_force , f_cv_lower_boundary , f_cv_upper_boundary , f_cv_hard_lower_boundary , f_cv_hard_upper_boundary , f_cv_reflecting_lower_boundary , f_cv_reflecting_upper_boundary , f_cv_grid , f_cv_runave , f_cv_corrfunc , f_cv_scripted , f_cv_custom_function , f_cv_periodic , f_cv_single_cvc , f_cv_scalar , f_cv_linear , f_cv_homogeneous , f_cv_multiple_ts , f_cv_ntot }

enum	features_cvc { f_cvc_active , f_cvc_scalar , f_cvc_periodic , f_cvc_width , f_cvc_lower_boundary , f_cvc_upper_boundary , f_cvc_explicit_atom_groups , f_cvc_gradient , f_cvc_explicit_gradient , f_cvc_inv_gradient , f_cvc_Jacobian , f_cvc_one_site_total_force , f_cvc_debug_gradient , f_cvc_pbc_minimum_image , f_cvc_com_based , f_cvc_scalable , f_cvc_scalable_com , f_cvc_collect_atom_ids , f_cvc_ntot }

enum	features_atomgroup { f_ag_active , f_ag_center , f_ag_center_origin , f_ag_rotate , f_ag_fitting_group , f_ag_explicit_gradient , f_ag_fit_gradients , f_ag_atom_forces , f_ag_scalable , f_ag_scalable_com , f_ag_collect_atom_ids , f_ag_ntot }

Protected Types inherited from colvarparse
enum	key_set_mode { key_not_set = 0 , key_set_user = 1 , key_set_default = 2 }
	How a keyword has been set.

Protected Types inherited from colvardeps
enum	feature_type { f_type_not_set , f_type_dynamic , f_type_user , f_type_static }
	Enum of possible feature types.

Protected Member Functions inherited from colvarparse
bool	get_key_string_value (std::string const &conf, char const *key, std::string &data)
	Get the string value of a keyword, and save it for later parsing.

bool	get_key_string_multi_value (std::string const &conf, char const *key, std::vector< std::string > &data)
	Get multiple strings from repeated instances of a same keyword.

template<typename TYPE >
bool	_get_keyval_scalar_ (std::string const &conf, char const *key, TYPE &value, TYPE const &def_value, Parse_Mode const &parse_mode)
	Template for single-value keyword parsers.

template<typename TYPE >
bool	_get_keyval_vector_ (std::string const &conf, char const *key, std::vector< TYPE > &values, std::vector< TYPE > const &def_values, Parse_Mode const &parse_mode)
	Template for multiple-value keyword parsers.

template<typename TYPE >
int	_get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, TYPE &value, TYPE const &def_value)
	Extract the value of a variable from a string.

template<typename TYPE >
int	_get_keyval_scalar_novalue_ (std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode)
	Handle the case where the user provides a keyword without value.

template<typename TYPE >
void	mark_key_set_user (std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode)
	Record that the keyword has just been user-defined.

template<typename TYPE >
void	mark_key_set_default (std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode)
	Record that the keyword has just been set to its default value.

void	error_key_required (std::string const &key_str, Parse_Mode const &parse_mode)
	Raise error condition due to the keyword being required!

bool	key_already_set (std::string const &key_str)
	True if the keyword has been set already.

void	add_keyword (char const *key)
	Add a new valid keyword to the list.

void	strip_values (std::string &conf)
	Remove all the values from the config string.

Protected Member Functions inherited from colvarparams
	colvarparams ()
	Default constructor.

virtual	~colvarparams ()
	Default destructor.

void	register_param (std::string const &param_name, void *param_ptr)
	Register the given parameter.

void	register_param_grad (std::string const &param_name, colvarvalue *param_grad_ptr)
	Register the gradient of the given parameter.

Protected Member Functions inherited from colvardeps
bool	get_keyval_feature (colvarparse cvp, std::string const &conf, char const key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)
	Parse a keyword and enable a feature accordingly.

Protected Attributes inherited from colvarparse
std::string const	keyword_delimiters_left
	Characters allowed immediately to the left of a kewyord.

std::string const	keyword_delimiters_right
	Characters allowed immediately to the right of a kewyord.

std::list< std::string >	allowed_keywords
	List of legal keywords for this object: this is updated by each call to colvarparse::get_keyval() or colvarparse::key_lookup()

std::map< std::string, key_set_mode >	key_set_modes
	Track which keywords have been already set, and how.

std::list< size_t >	data_begin_pos
	List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.

std::list< size_t >	data_end_pos
	List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.

std::string	config_string
	Configuration string of the object (includes comments)

Protected Attributes inherited from colvarparams
std::map< std::string, void const * >	param_map
	Pointers to relevant parameters that may be accessed by other objects.

std::map< std::string, colvarvalue const * >	param_grad_map
	Derivatives of the object with respect to internal parameters.

Protected Attributes inherited from colvardeps
int	time_step_factor

std::vector< feature_state >	feature_states
	List of the states of all features.

Detailed Description

Store the information of a group of atoms in a structure-of-arrays (SoA) style.

This class keeps the information of a group of atoms. These information includes the internal indices in the colvarproxy class, positions, charges, velocities, masses, gradients, total forces and atom IDs of all atoms in the atom group. The memory layout of this class is different from the traditional cvm::atom_group class as this class uses the SoA layout to group each atom properties in their own array instead of using a single array of cvm::atom (array-of-structures or AoS). According to various micro-benchmarks, the use of SoA can significantly improve the performance. There are two disadvantages of adopting SoA:

The insertion or delete of atoms in an object of cvm::atom_group is not as handy as the AoS class cvm::atom_group. To solve this issue, this nested class cvm::atom_group::atom_modifier has been implemented as a temporary AoS class that shares the same interfaces like cvm::atom_group::atom_modifier::add_atom_numbers as the traditional AoS class cvm::atom_group. To add or remove atoms in the SoA class, you can do the following:
{

auto modify_atoms = atoms->get_atom_modifier();

modify_atoms->add_atom_numbers(conf);

}

Specifically, when get_atom_modifier is called, the temporary AoS atom group will be created based on this SoA atom group, and after the modification of the temporary AoS atom group is completed, the destructor cvm::atom_group::atom_modifier::~atom_modifier will synchronize the changes back to this SoA atom group.
It would be difficult to reorder the atoms inside an SoA group. In MD engines that need to move atoms between cells/patches (like NAMD), it is better to transform the atoms back to AoS before moving (migration). Fortunately Colvars does not need this as the order of atoms inside a group never changes.

Constructor & Destructor Documentation

◆ atom_group()

cvm::atom_group::atom_group ( )

Default constructor.

Attention: Will call init_dependencies() to initialize the dependency tree.

◆ ~atom_group()

cvm::atom_group::~atom_group ( )

override

Destructor.

Attention: Will call clear_soa() to de-reference all atoms (if not scalable) from the proxy class.

Member Function Documentation

◆ apply_colvar_force()

void cvm::atom_group::apply_colvar_force ( cvm::real const & force )

Used by a (scalar) colvar to apply its force on its atom_group members.

The (scalar) force is multiplied by the colvar gradient for each atom; this should be used when a colvar with scalar colvarvalue type is used (this is the most frequent case: for colvars with a non-scalar type, the most convenient solution is to sum together the Cartesian forces from all the colvar components, and use apply_force() or apply_forces()). If the group is being rotated to a reference frame (e.g. to express the colvar independently from the solute rotation), the gradients are temporarily rotated to the original frame.

◆ apply_force()

void cvm::atom_group::apply_force ( cvm::rvector const & force )

Apply a force "to the center of mass", i.e. the force is distributed on each atom according to its mass.

If the group is being rotated to a reference frame (e.g. to express the colvar independently from the solute rotation), the force is rotated back to the original frame. Colvar gradients are not used, either because they were not defined (e.g because the colvar has not a scalar value) or the biases require to micromanage the force. This function will be phased out eventually, in favor of apply_colvar_force() once that is implemented for non-scalar values

◆ calc_fit_forces()

template<typename main_force_accessor_T , typename fitting_force_accessor_T >

void cvm::atom_group::calc_fit_forces	(	main_force_accessor_T	accessor_main,
		fitting_force_accessor_T	accessor_fitting
	)		const

Calculate or apply the fitting group forces from the main group forces.

Template Parameters

main_force_accessor_T	The type of accessor of the main group forces or gradients.
fitting_force_accessor_T	The type of accessor of the fitting group forces or gradients.

Parameters

accessor_main	The accessor of the main group forces or gradients. accessor_main(i) should return the i-th force or gradient of the main group.
accessor_fitting	The accessor of the fitting group forces or gradients. accessor_fitting(j, v) should store/apply the j-th atom gradient or force in the fitting group.

This function just dispatches the parameters to calc_fit_forces_impl that really performs the calculations.

◆ calc_fit_forces_impl()

template<bool B_ag_center, bool B_ag_rotate, typename main_force_accessor_T , typename fitting_force_accessor_T >

void cvm::atom_group::calc_fit_forces_impl	(	main_force_accessor_T	accessor_main,
		fitting_force_accessor_T	accessor_fitting
	)		const

Actual implementation of calc_fit_gradients and calc_fit_forces. The template is used to avoid branching inside the loops in case that the CPU branch prediction is broken (or further migration to GPU code).

Template Parameters

B_ag_center	Centered the reference to origin? This should follow the value of `is_enabled(f_ag_center)`.
B_ag_rotate	Calculate the optimal rotation? This should follow the value of `is_enabled(f_ag_rotate)`.
main_force_accessor_T	The type of accessor of the main group forces or gradients acting on the rotated frame.
fitting_force_accessor_T	The type of accessor of the fitting group forces or gradients.

Parameters

accessor_main	The accessor of the main group forces or gradients. accessor_main(i) should return the i-th force or gradient of the rotated main group.
accessor_fitting	The accessor of the fitting group forces or gradients. accessor_fitting(j, v) should store/apply the j-th atom gradient or force in the fitting group.

This function is used to (i) project the gradients of CV with respect to rotated main group atoms to fitting group atoms, or (ii) project the forces on rotated main group atoms to fitting group atoms, by the following two steps (using the goal (ii) for example): (1) Loop over the positions of main group atoms and call cvm::quaternion::position_derivative_inner to project the forces on rotated main group atoms to the forces on quaternion. (2) Loop over the positions of fitting group atoms, compute the gradients of \(\mathbf{q}\) with respect to the position of each atom, and then multiply that with the force on \(\mathbf{q}\) (chain rule).

◆ center_ref_pos()

void cvm::atom_group::center_ref_pos ( )

Save aside the center of geometry of the reference positions, then subtract it from them.

In this way it will be possible to use ref_pos also for the rotational fit. This is called either by atom_group::parse or by CVCs that assign reference positions (eg. RMSD, eigenvector).

◆ clear_soa()

void cvm::atom_group::clear_soa ( )

Remove all atoms from this SoA group and the proxy.

Attention: atoms_ids , sorted_atoms_ids , sorted_atoms_ids_map total mass, total charge, reference positions and the fitting group are kept.

◆ do_feature_side_effects()

void cvm::atom_group::do_feature_side_effects ( int id )

overridevirtual

Implements possible actions to be carried out when a given feature is enabled This overloads the base function in colvardeps

Reimplemented from colvardeps.

◆ features()

const std::vector< feature * > & cvm::atom_group::features ( ) const

inlineoverridevirtual

Implementation of the feature list accessor for atom group.

Implements colvardeps.

◆ get_atom_modifier()

atom_modifier cvm::atom_group::get_atom_modifier ( )

inline

Get the atom modifier object associated with this SoA atom group.

Attention: You can get only one instance of cvm::atom_group::atom_modifier in a scope. To prevent acquiring multiple instances of atom_modifier at the same time which may corrupt the SoA layout. The associated cvm::atom_group::atom_modifier will try locking mutex_lock.

◆ init_atom_from_proxy() [1/3]

cvm::atom_group::simple_atom cvm::atom_group::init_atom_from_proxy	(	colvarproxy *const	p,
		const simple_atom &	atom
	)

static

Initialize an instance of cvm::atom_group::simple_atom from colvarproxy.

Parameters

p	The pointer to the `colvarproxy` instance.
simple_atom	The existing object of `cvm::atom_group::simple_atom`

Attention: The cvm::atom_group::simple_atom::proxy_index of input atom must be known. The reference count in the proxy will be increased.

◆ init_atom_from_proxy() [2/3]

cvm::atom_group::simple_atom cvm::atom_group::init_atom_from_proxy	(	colvarproxy *const	p,
		cvm::residue_id const &	residue,
		std::string const &	atom_name,
		std::string const &	segment_id
	)

static

Initialize an instance of cvm::atom_group::simple_atom from colvarproxy.

Parameters

p	The pointer to the `colvarproxy` instance.
residue	The residue number of the atom
atom_name	The name of the atom in the residue
segment_id	For PSF topologies, the segment identifier; for other type of topologies, may not be required

◆ init_atom_from_proxy() [3/3]

cvm::atom_group::simple_atom cvm::atom_group::init_atom_from_proxy	(	colvarproxy *const	p,
		int	atom_number
	)

static

Initialize an instance of cvm::atom_group::simple_atom from colvarproxy.

Parameters

p	The pointer to the `colvarproxy` instance.
atom_number	Atom index in the system topology (1-based)

◆ init_dependencies()

int cvm::atom_group::init_dependencies ( )

overridevirtual

Initialize dependency tree.

Implements colvardeps.

◆ modify_features()

std::vector< feature * > & cvm::atom_group::modify_features ( )

inlineoverridevirtual

Implements colvardeps.

◆ overlap()

int cvm::atom_group::overlap	(	const atom_group &	g1,
		const atom_group &	g2
	)

static

Detect whether two groups share atoms.

If yes, returns 1-based number of a common atom; else, returns 0

◆ print_properties()

void cvm::atom_group::print_properties	(	std::string const &	colvar_name,
		int	i,
		int	j
	)

Print the updated the total mass and charge of a group.

This is needed in case the hosting MD code has an option to change atom masses after their initialization.

◆ read_total_forces()

void cvm::atom_group::read_total_forces ( )

Get the current total_forces.

this must be called always after read_positions(); if f_ag_rotate is defined, the same rotation applied to the coordinates will be used.

◆ read_velocities()

void cvm::atom_group::read_velocities ( )

Get the current velocities.

this must be called always after read_positions(); if f_ag_rotate is defined, the same rotation applied to the coordinates will be used.

◆ setup()

int cvm::atom_group::setup ( )

Update data required to calculate cvc's.

The data updated includes atomic charges and masses, and also the total charge and total mass of this atom group.

◆ sorted_ids()

std::vector< int > const & cvm::atom_group::sorted_ids ( ) const

inline

Sorted internal atom IDs (populated on-demand by create_sorted_ids);.

Used to read coordinate files

The documentation for this class was generated from the following files:

colvaratoms.h
colvaratoms.cpp

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ atom_group()

◆ ~atom_group()

Member Function Documentation

◆ apply_colvar_force()

◆ apply_force()

◆ calc_fit_forces()

◆ calc_fit_forces_impl()

◆ center_ref_pos()

◆ clear_soa()

◆ do_feature_side_effects()

◆ features()

◆ get_atom_modifier()

◆ init_atom_from_proxy() [1/3]

◆ init_atom_from_proxy() [2/3]

◆ init_atom_from_proxy() [3/3]

◆ init_dependencies()

◆ modify_features()

◆ overlap()

◆ print_properties()

◆ read_total_forces()

◆ read_velocities()

◆ setup()

◆ sorted_ids()