Collective Variables Module - Developer Documentation
Public Member Functions | Protected Attributes | List of all members
colvar::distance_z Class Reference

Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*)) More...

#include <colvarcomp.h>

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Public Member Functions

 distance_z (std::string const &conf)
 
virtual void calc_value ()
 Calculate the variable.
 
virtual void calc_gradients ()
 Calculate the atomic gradients, to be reused later in order to apply forces.
 
virtual void calc_force_invgrads ()
 Calculate the total force from the system using the inverse atomic gradients.
 
virtual void calc_Jacobian_derivative ()
 Calculate the divergence of the inverse atomic gradients.
 
virtual void apply_force (colvarvalue const &force)
 Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) More...
 
virtual cvm::real dist2 (colvarvalue const &x1, colvarvalue const &x2) const
 Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities) More...
 
virtual colvarvalue dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
 Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities)
 
virtual colvarvalue dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
 Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities)
 
virtual void wrap (colvarvalue &x) const
 Redefined to make use of the user-provided period.
 
- Public Member Functions inherited from colvar::cvc
 cvc (std::string const &conf)
 Constructor. More...
 
cvm::atom_groupparse_group (std::string const &conf, char const *group_key, bool optional=false)
 Within the constructor, make a group parse its own options from the provided configuration string Returns reference to new group.
 
virtual int init_total_force_params (std::string const &conf)
 Parse options pertaining to total force calculation.
 
int setup ()
 After construction, set data related to dependency handling.
 
 cvc ()
 Default constructor (used when cvc objects are declared within other ones)
 
virtual ~cvc ()
 Destructor.
 
virtual const std::vector< feature * > & features ()
 Implementation of the feature list accessor for colvar.
 
virtual std::vector< feature * > & modify_features ()
 
virtual void read_data ()
 Obtain data needed for the calculation for the backend.
 
void calc_fit_gradients ()
 Calculate the atomic fit gradients.
 
virtual void debug_gradients ()
 Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component.
 
colvarvalue const & value () const
 Return the previously calculated value.
 
colvarvalue const & total_force () const
 Return the previously calculated total force.
 
colvarvalue const & Jacobian_derivative () const
 Return the previously calculated divergence of the inverse atomic gradients.
 
void register_atom_group (cvm::atom_group *ag)
 Store a pointer to new atom group, and list as child for dependencies.
 
- Public Member Functions inherited from colvarparse
 colvarparse (const std::string &conf)
 Constructor that stores the object's config string.
 
void init ()
 Set the object ready to parse a new configuration string.
 
void init (const std::string &conf)
 Set a new config string for this object.
 
const std::string & get_config ()
 
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=(int) 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=(size_t) 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, 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=(cvm::real) 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,(int) 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,(size_t) 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,(long) 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,(cvm::real) 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=NULL, size_t *save_pos=NULL)
 Low-level function for parsing configuration strings; automatically adds the requested keyword to the list of valid ones. More...
 
bool brace_check (std::string const &conf, size_t const start_pos=0)
 Check if the content of the file has matching braces.
 
- 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=f_type_not_set)
 Pair a numerical feature ID with a description and type.
 
bool is_dynamic (int id)
 
bool is_static (int id)
 
bool is_user (int id)
 
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)
 
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 id)
 
void init_cvb_requires ()
 
void init_cv_requires ()
 
void init_cvc_requires ()
 
void init_ag_requires ()
 
void print_state ()
 print all enabled features and those of children, for debugging
 

Protected Attributes

cvm::atom_groupmain
 Main atom group.
 
cvm::atom_groupref1
 Reference atom group.
 
cvm::atom_groupref2
 Optional, second ref atom group.
 
bool b_no_PBC
 Use absolute positions, ignoring PBCs when present.
 
cvm::rvector axis
 Vector on which the distance vector is projected.
 
cvm::real axis_norm
 Norm of the axis.
 
cvm::rvector dist_v
 Vector distance, cached to be recycled.
 
bool fixed_axis
 Flag: using a fixed axis vector?
 
- Protected Attributes inherited from colvar::cvc
colvarvalue x
 Cached value.
 
colvarvalue x_old
 Value at the previous step.
 
colvarvalue ft
 Calculated total force (Note: this is calculated from the total atomic forces read from the program, subtracting fromt the "internal" forces of the system the "external" forces from the colvar biases)
 
colvarvalue jd
 Calculated Jacobian derivative (divergence of the inverse gradients): serves to calculate the phase space correction.
 
- Protected Attributes inherited from colvardeps
int time_step_factor
 

Additional Inherited Members

- Public Types inherited from colvarparse
enum  Parse_Mode { parse_normal, parse_silent }
 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_apply_force, f_cvb_get_total_force,
  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_ntot
}
 
enum  features_colvar {
  f_cv_active, f_cv_awake, f_cv_gradient, f_cv_collect_gradient,
  f_cv_fdiff_velocity, f_cv_total_force, f_cv_total_force_calc, f_cv_subtract_applied_force,
  f_cv_Jacobian, f_cv_hide_Jacobian, f_cv_extended_Lagrangian, 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_grid,
  f_cv_runave, f_cv_corrfunc, f_cv_scripted, f_cv_custom_function,
  f_cv_periodic, 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_gradient, f_cvc_implicit_gradient,
  f_cvc_inv_gradient, f_cvc_debug_gradient, f_cvc_Jacobian, f_cvc_pbc_minimum_image,
  f_cvc_one_site_total_force, f_cvc_com_based, f_cvc_scalable, f_cvc_scalable_com,
  f_cvc_ntot
}
 
enum  features_atomgroup {
  f_ag_active, f_ag_center, f_ag_rotate, f_ag_fitting_group,
  f_ag_implicit_gradient, f_ag_fit_gradients, f_ag_atom_forces, f_ag_scalable,
  f_ag_scalable_com, f_ag_ntot
}
 
- Static Public Member Functions inherited from colvar::cvc
static void delete_features ()
 
- 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.
 
- Public Attributes inherited from colvar::cvc
std::string name
 The name of the object (helps to identify this cvc instance when debugging)
 
std::string function_type
 Description of the type of collective variable. More...
 
cvm::real sup_coeff
 Coefficient in the polynomial combination (default: 1.0)
 
int sup_np
 Exponent in the polynomial combination (default: 1)
 
bool b_periodic
 Is this a periodic component?
 
cvm::real period
 Period of this cvc value, (default: 0.0, non periodic)
 
cvm::real wrap_center
 If the component is periodic, wrap around this value (default: 0.0)
 
std::vector< cvm::atom_group * > atom_groups
 Pointers to all atom groups, to let colvars collect info e.g. atomic gradients.
 
bool b_try_scalable
 Whether or not this CVC will be computed in parallel whenever possible.
 
- Public Attributes inherited from colvardeps
std::string description
 
- Static Public Attributes inherited from colvar::cvc
static std::vector< feature * > cvc_features
 Implementation of the feature list for colvar.
 
- Static Public Attributes inherited from colvarparse
static const char *const white_space = " \t"
 Accepted white space delimiters, used in key_lookup()
 
- Protected Member Functions inherited from colvarparse
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)
 
bool _get_keyval_scalar_string_ (std::string const &conf, char const *key, std::string &value, std::string const &def_value, Parse_Mode const parse_mode)
 
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)
 
- 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.
 

Detailed Description

Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*))

Member Function Documentation

◆ apply_force()

void colvar::distance_z::apply_force ( colvarvalue const &  cvforce)
virtual

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function)

Note: multiple calls to this function within the same simulation step will add the forces altogether

Parameters
cvforceThe collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object

Implements colvar::cvc.

Reimplemented in colvar::distance_xy.

◆ dist2()

cvm::real colvar::distance_z::dist2 ( colvarvalue const &  x1,
colvarvalue const &  x2 
) const
virtual

Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities)

colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object.

If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients.

If constraints are present (and not already implemented by any of the colvarvalue types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface.

Finally, another useful application, if you are performing very many operations with these functions, could be to override the colvarvalue member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar colvarvalue type.

Reimplemented from colvar::cvc.

Reimplemented in colvar::distance_xy.


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