Collective Variables Module - Developer Documentation
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colvarvalue Class Reference

Value of a collective variable: this is a metatype which can be set at runtime. By default it is set to be a scalar number, and can be treated as such in all operations (this is done by most cvc implementations). More...

#include <colvarvalue.h>

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Public Types

enum  Type {
  type_notset, type_scalar, type_3vector, type_unit3vector,
  type_unit3vectorderiv, type_quaternion, type_quaternionderiv, type_vector,
  type_all
}
 Possible types of value. More...
 

Public Member Functions

size_t size () const
 Number of dimensions of this variable.
 
 colvarvalue ()
 Default constructor: this class defaults to a scalar number and always behaves like it unless you change its type.
 
 colvarvalue (Type const &vti)
 Constructor from a type specification.
 
 colvarvalue (cvm::real const &x)
 Copy constructor from real base type.
 
 colvarvalue (cvm::rvector const &v, Type vti=type_3vector)
 Copy constructor from rvector base type (Note: this sets by default a type type_3vector , if you want a type_unit3vector you must set it explicitly)
 
 colvarvalue (cvm::quaternion const &q, Type vti=type_quaternion)
 Copy constructor from quaternion base type.
 
 colvarvalue (cvm::vector1d< cvm::real > const &v, Type vti=type_vector)
 Copy constructor from vector1d base type.
 
 colvarvalue (colvarvalue const &x)
 Copy constructor from another colvarvalue.
 
void reset ()
 Set to the null value for the data type currently defined.
 
void apply_constraints ()
 If the variable has constraints (e.g. unitvector or quaternion), transform it to satisfy them; this function needs to be called only when the colvarvalue is calculated outside of cvc objects.
 
Type type () const
 Get the current type.
 
void type (Type const &vti)
 Set the type explicitly.
 
void type (colvarvalue const &x)
 Set the type after another colvarvalue.
 
void is_derivative ()
 
cvm::real norm2 () const
 Square norm of this colvarvalue.
 
cvm::real norm () const
 Norm of this colvarvalue.
 
cvm::real dist2 (colvarvalue const &x2) const
 Square distance between this colvarvalue and another.
 
colvarvalue dist2_grad (colvarvalue const &x2) const
 Derivative with respect to this colvarvalue of the square distance.
 
colvarvalueoperator= (colvarvalue const &x)
 Assignment operator (type of x is checked)
 
void operator+= (colvarvalue const &x)
 
void operator-= (colvarvalue const &x)
 
void operator*= (cvm::real const &a)
 
void operator/= (cvm::real const &a)
 
 operator cvm::real () const
 
 operator cvm::rvector () const
 
 operator cvm::quaternion () const
 
cvm::vector1d< cvm::real > const as_vector () const
 
bool is_scalar () const
 Whether this variable is a real number.
 
void add_elem (colvarvalue const &x)
 
colvarvalue const get_elem (int const i_begin, int const i_end, Type const vt) const
 Get a single colvarvalue out of elements of the vector.
 
void set_elem (int const i_begin, int const i_end, colvarvalue const &x)
 Set elements of the vector from a single colvarvalue.
 
void set_random ()
 Make each element a random number in N(0,1)
 
colvarvalue const get_elem (int const icv) const
 Get a single colvarvalue out of elements of the vector.
 
void set_elem (int const icv, colvarvalue const &x)
 Set elements of the vector from a single colvarvalue.
 
cvm::real operator[] (int const i) const
 Get a scalar number out of an element of the vector.
 
cvm::realoperator[] (int const i)
 Use an element of the vector as a scalar number.
 
void undef_op () const
 Undefined operation.
 
size_t output_width (size_t const &real_width) const
 
std::string to_simple_string () const
 Formats value as a script-friendly string (space separated list)
 
int from_simple_string (std::string const &s)
 Parses value from a script-friendly string (space separated list)
 

Static Public Member Functions

static bool type_checking ()
 Whether or not the type check is enforced.
 
static std::string const type_desc (Type t)
 Runtime description of value types.
 
static std::string const type_keyword (Type t)
 User keywords for specifying value types in the configuration.
 
static size_t num_df (Type t)
 Number of degrees of freedom for each supported type.
 
static size_t num_dimensions (Type t)
 Number of dimensions for each supported type (used to allocate vector1d_value)
 
static colvarvalue const interpolate (colvarvalue const &x1, colvarvalue const &x2, cvm::real const lambda=0.5)
 
static int check_types (colvarvalue const &x1, colvarvalue const &x2)
 Ensure that the two types are the same within a binary operator.
 
static int check_types_assign (Type const &vt1, Type const &vt2)
 Ensure that the two types are the same within an assignment, or that the left side is type_notset.
 
static void inner_opt (colvarvalue const &x, std::vector< colvarvalue >::iterator &xv, std::vector< colvarvalue >::iterator const &xv_end, std::vector< cvm::real >::iterator &result)
 Optimized routine for the inner product of one collective variable with an array.
 
static void inner_opt (colvarvalue const &x, std::list< colvarvalue >::iterator &xv, std::list< colvarvalue >::iterator const &xv_end, std::vector< cvm::real >::iterator &result)
 Optimized routine for the inner product of one collective variable with an array.
 
static void p2leg_opt (colvarvalue const &x, std::vector< colvarvalue >::iterator &xv, std::vector< colvarvalue >::iterator const &xv_end, std::vector< cvm::real >::iterator &result)
 Optimized routine for the second order Legendre polynomial, (3cos^2(w)-1)/2, of one collective variable with an array.
 
static void p2leg_opt (colvarvalue const &x, std::list< colvarvalue >::iterator &xv, std::list< colvarvalue >::iterator const &xv_end, std::vector< cvm::real >::iterator &result)
 Optimized routine for the second order Legendre polynomial of one collective variable with an array.
 

Public Attributes

Type value_type
 Current type of this colvarvalue object.
 
cvm::real real_value
 Real data member.
 
cvm::rvector rvector_value
 3-dimensional vector data member
 
cvm::quaternion quaternion_value
 Quaternion data member.
 
cvm::vector1d< cvm::realvector1d_value
 Generic vector data member.
 
std::vector< Typeelem_types
 If vector1d_value is a concatenation of colvarvalues, keep track of the individual types.
 
std::vector< int > elem_indices
 If vector1d_value is a concatenation of colvarvalues, these mark the initial components of each colvarvalue.
 
std::vector< int > elem_sizes
 If vector1d_value is a concatenation of colvarvalues, these mark how many components for each colvarvalue.
 

Friends

colvarvalue operator+ (colvarvalue const &x1, colvarvalue const &x2)
 
colvarvalue operator- (colvarvalue const &x1, colvarvalue const &x2)
 
colvarvalue operator* (colvarvalue const &x, cvm::real const &a)
 
colvarvalue operator* (cvm::real const &a, colvarvalue const &x)
 
colvarvalue operator/ (colvarvalue const &x, cvm::real const &a)
 
cvm::real operator* (colvarvalue const &x1, colvarvalue const &x2)
 Inner product.
 
std::ostream & operator<< (std::ostream &os, colvarvalue const &q)
 Formatted output operator.
 
std::istream & operator>> (std::istream &is, colvarvalue &q)
 Formatted input operator.
 

Detailed Description

Value of a collective variable: this is a metatype which can be set at runtime. By default it is set to be a scalar number, and can be treated as such in all operations (this is done by most cvc implementations).

colvarvalue allows colvar to be treat different data types. By default, a colvarvalue variable is a scalar number. To use it as another type, declare and initialize it as

colvarvalue x(colvarvalue::type_xxx)

, use (colvarvalue::type_xxx) at a later stage, or if unset, assign the type with

x = y;

, provided y is correctly set.

All operators (either unary or binary) on a colvarvalue object performs one or more checks on the Type, except when reading from a stream, when there is no way to detect the Type. To use

is >> x;

x MUST already have a type correcly set up for properly parsing the stream. No problem of course with the output streams:

os << x;

Note on performance: to avoid type checks in a long array of colvarvalue objects, use one of the existing "_opt" functions or implement a new one

Member Enumeration Documentation

◆ Type

Possible types of value.

These three cover most possibilities of data type one can devise. If you need to implement a new colvar with a very complex data type, it's better to put an allocatable class here

Enumerator
type_notset 

Undefined type.

type_scalar 

Scalar number, implemented as colvarmodule::real (default)

type_3vector 

3-dimensional vector, implemented as colvarmodule::rvector

type_unit3vector 

3-dimensional unit vector, implemented as colvarmodule::rvector

type_unit3vectorderiv 

3-dimensional vector that is a derivative of a unitvector

type_quaternion 

4-dimensional unit vector representing a rotation, implemented as colvarmodule::quaternion

type_quaternionderiv 

4-dimensional vector that is a derivative of a quaternion

type_vector 

vector (arbitrary dimension)

type_all 

Needed to iterate through enum.

Member Function Documentation

◆ add_elem()

void colvarvalue::add_elem ( colvarvalue const &  x)

Add an element to the vector (requires that type_vector is already set). This is only needed to use this object as a vector of "complex" colvar values. To use it instead as a plain n-dimensional vector, access vector1d_value directly.

◆ interpolate()

colvarvalue const colvarvalue::interpolate ( colvarvalue const &  x1,
colvarvalue const &  x2,
cvm::real const  lambda = 0.5 
)
static

Return the midpoint between x1 and x2, optionally weighted by lambda (which must be between 0.0 and 1.0)

◆ is_derivative()

void colvarvalue::is_derivative ( )

Make the type a derivative of the original type (so that its constraints do not apply)

◆ output_width()

size_t colvarvalue::output_width ( size_t const &  real_width) const

Give the number of characters required to output this colvarvalue, given the current type assigned and the number of characters for a real number


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