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lammps/lib/colvars/colvarvalue.h

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// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#ifndef COLVARVALUE_H
#define COLVARVALUE_H
#include "colvarmodule.h"
#include "colvartypes.h"
/// \brief 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 \link cvc \endlink implementations).
///
/// \link colvarvalue \endlink allows \link colvar \endlink to be
/// treat different data types. By default, a \link colvarvalue
/// \endlink variable is a scalar number. To use it as
/// another type, declare and initialize it as
/// \code colvarvalue x(colvarvalue::type_xxx)\endcode, use \link x.type
/// (colvarvalue::type_xxx) \endlink at a later stage, or if unset,
/// assign the type with \code x = y; \endcode, provided y is correctly set.
///
/// All operators (either unary or binary) on a \link
/// colvarvalue \endlink object performs one or more checks on the
/// \link Type \endlink, except when reading from a stream, when there is no way to
/// detect the \link Type \endlink. To use \code is >> x; \endcode x \b MUST
/// already have a type correcly set up for properly parsing the
/// stream. No problem of course with the output streams: \code os << x; \endcode
///
/// \em Note \em on \em performance: to avoid type checks in a long array of \link
/// colvarvalue \endlink objects, use one of the existing "_opt" functions or implement a new one
class colvarvalue {
public:
/// \brief 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
enum Type {
/// Undefined type
type_notset,
/// Scalar number, implemented as \link colvarmodule::real \endlink (default)
type_scalar,
/// 3-dimensional vector, implemented as \link colvarmodule::rvector \endlink
type_3vector,
/// 3-dimensional unit vector, implemented as \link colvarmodule::rvector \endlink
type_unit3vector,
/// 3-dimensional vector that is a derivative of a unitvector
type_unit3vectorderiv,
/// 4-dimensional unit vector representing a rotation, implemented as \link colvarmodule::quaternion \endlink
type_quaternion,
/// 4-dimensional vector that is a derivative of a quaternion
type_quaternionderiv,
/// vector (arbitrary dimension)
type_vector,
/// Needed to iterate through enum
type_all
};
/// Current type of this colvarvalue object
Type value_type;
/// \brief Real data member
cvm::real real_value;
/// \brief 3-dimensional vector data member
cvm::rvector rvector_value;
/// \brief Quaternion data member
cvm::quaternion quaternion_value;
/// \brief Generic vector data member
cvm::vector1d<cvm::real> vector1d_value;
/// \brief If \link vector1d_value \endlink is a concatenation of colvarvalues,
/// keep track of the individual types
std::vector<Type> elem_types;
/// \brief If \link vector1d_value \endlink is a concatenation of colvarvalues,
/// these mark the initial components of each colvarvalue
std::vector<int> elem_indices;
/// \brief If \link vector1d_value \endlink is a concatenation of colvarvalues,
/// these mark how many components for each colvarvalue
std::vector<int> elem_sizes;
/// \brief Whether or not the type check is enforced
static inline bool type_checking()
{
return true;
}
/// Runtime description of value types
static std::string const type_desc(Type t);
/// User keywords for specifying value types in the configuration
static std::string const type_keyword(Type t);
/// Number of degrees of freedom for each supported type
static size_t num_df(Type t);
/// Number of dimensions for each supported type (used to allocate vector1d_value)
static size_t num_dimensions(Type t);
/// Number of dimensions of this variable
size_t size() const;
/// \brief Default constructor: this class defaults to a scalar
/// number and always behaves like it unless you change its type
inline colvarvalue()
: value_type(type_scalar), real_value(0.0)
{}
/// Constructor from a type specification
inline colvarvalue(Type const &vti)
: value_type(vti)
{
reset();
}
/// Copy constructor from real base type
inline colvarvalue(cvm::real const &x)
: value_type(type_scalar), real_value(x)
{}
/// \brief Copy constructor from rvector base type (Note: this sets
/// by default a type \link type_3vector \endlink , if you want a
/// \link type_unit3vector \endlink you must set it explicitly)
inline colvarvalue(cvm::rvector const &v, Type vti = type_3vector)
: value_type(vti), rvector_value(v)
{}
/// \brief Copy constructor from quaternion base type
inline colvarvalue(cvm::quaternion const &q, Type vti = type_quaternion)
: value_type(vti), quaternion_value(q)
{}
/// Copy constructor from vector1d base type
colvarvalue(cvm::vector1d<cvm::real> const &v, Type vti = type_vector);
/// Copy constructor from another \link colvarvalue \endlink
colvarvalue(colvarvalue const &x);
/// Set to the null value for the data type currently defined
void reset();
/// \brief If the variable has constraints (e.g. unitvector or
/// quaternion), transform it to satisfy them; this function needs
/// to be called only when the \link colvarvalue \endlink
/// is calculated outside of \link cvc \endlink objects
void apply_constraints();
/// Get the current type
inline Type type() const
{
return value_type;
}
/// Set the type explicitly
void type(Type const &vti);
/// Set the type after another \link colvarvalue \endlink
void type(colvarvalue const &x);
/// Make the type a derivative of the original type
/// (so that its constraints do not apply)
void is_derivative();
/// Square norm of this colvarvalue
cvm::real norm2() const;
/// Norm of this colvarvalue
inline cvm::real norm() const
{
return std::sqrt(this->norm2());
}
/// Square distance between this \link colvarvalue \endlink and another
cvm::real dist2(colvarvalue const &x2) const;
/// Derivative with respect to this \link colvarvalue \endlink of the square distance
colvarvalue dist2_grad(colvarvalue const &x2) const;
/// Return the midpoint between x1 and x2, optionally weighted by lambda
/// (which must be between 0.0 and 1.0)
static colvarvalue const interpolate(colvarvalue const &x1,
colvarvalue const &x2,
cvm::real const lambda = 0.5);
/// Assignment operator (type of x is checked)
colvarvalue & operator = (colvarvalue const &x);
void operator += (colvarvalue const &x);
void operator -= (colvarvalue const &x);
void operator *= (cvm::real const &a);
void operator /= (cvm::real const &a);
// Binary operators (return values)
friend colvarvalue operator + (colvarvalue const &x1, colvarvalue const &x2);
friend colvarvalue operator - (colvarvalue const &x1, colvarvalue const &x2);
friend colvarvalue operator * (colvarvalue const &x, cvm::real const &a);
friend colvarvalue operator * (cvm::real const &a, colvarvalue const &x);
friend colvarvalue operator / (colvarvalue const &x, cvm::real const &a);
/// Inner product
friend cvm::real operator * (colvarvalue const &x1, colvarvalue const &x2);
// Cast to scalar
inline operator cvm::real() const
{
if (value_type != type_scalar) {
cvm::error("Error: trying to use a variable of type \""+
type_desc(value_type)+"\" as one of type \""+
type_desc(type_scalar)+"\".\n");
}
return real_value;
}
// Cast to 3-vector
inline operator cvm::rvector() const
{
if ((value_type != type_3vector) &&
(value_type != type_unit3vector) &&
(value_type != type_unit3vectorderiv)) {
cvm::error("Error: trying to use a variable of type \""+
type_desc(value_type)+"\" as one of type \""+
type_desc(type_3vector)+"\".\n");
}
return rvector_value;
}
// Cast to quaternion
inline operator cvm::quaternion() const
{
if ((value_type != type_quaternion) &&
(value_type != type_quaternionderiv)) {
cvm::error("Error: trying to use a variable of type \""+
type_desc(value_type)+"\" as one of type \""+
type_desc(type_quaternion)+"\".\n");
}
return quaternion_value;
}
// Create a n-dimensional vector from one of the basic types, or return the existing vector
cvm::vector1d<cvm::real> const as_vector() const;
/// Whether this variable is a real number
inline bool is_scalar() const
{
return (value_type == type_scalar);
}
/// 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.
void add_elem(colvarvalue const &x);
/// Get a single colvarvalue out of elements of the vector
colvarvalue const get_elem(int const i_begin, int const i_end, Type const vt) const;
/// Set elements of the vector from a single colvarvalue
void set_elem(int const i_begin, int const i_end, colvarvalue const &x);
/// Make each element a random number in N(0,1)
void set_random();
/// Get a single colvarvalue out of elements of the vector
colvarvalue const get_elem(int const icv) const;
/// Set elements of the vector from a single colvarvalue
void set_elem(int const icv, colvarvalue const &x);
/// Get a scalar number out of an element of the vector
cvm::real operator [] (int const i) const;
/// Use an element of the vector as a scalar number
cvm::real & operator [] (int const i);
/// Ensure that the two types are the same within a binary operator
static int check_types(colvarvalue const &x1, colvarvalue const &x2);
/// Ensure that the two types are the same within an assignment, or that the left side is type_notset
static int check_types_assign(Type const &vt1, Type const &vt2);
/// Undefined operation
void undef_op() const;
/// \brief Formatted output operator
friend std::ostream & operator << (std::ostream &os, colvarvalue const &q);
/// \brief Formatted input operator
friend std::istream & operator >> (std::istream &is, colvarvalue &q);
/// Give the number of characters required to output this
/// colvarvalue, given the current type assigned and the number of
/// characters for a real number
size_t output_width(size_t const &real_width) const;
/// Formats value as a script-friendly string (space separated list)
std::string to_simple_string() const;
/// Parses value from a script-friendly string (space separated list)
int from_simple_string(std::string const &s);
// optimized routines for operations on arrays of colvar values;
// xv and result are assumed to have the same number of elements
/// \brief Optimized routine for the inner product of one collective
/// variable with an array
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);
/// \brief 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);
/// \brief 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::vector<colvarvalue>::iterator &xv,
std::vector<colvarvalue>::iterator const &xv_end,
std::vector<cvm::real>::iterator &result);
/// \brief Optimized routine for the second order Legendre
/// polynomial 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);
};
inline size_t colvarvalue::size() const
{
switch (value_type) {
case colvarvalue::type_notset:
default:
return 0; break;
case colvarvalue::type_scalar:
return 1; break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return 3; break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return 4; break;
case colvarvalue::type_vector:
return vector1d_value.size(); break;
}
}
inline cvm::real colvarvalue::operator [] (int const i) const
{
switch (value_type) {
case colvarvalue::type_notset:
default:
cvm::error("Error: trying to access a colvar value "
"that is not initialized.\n", BUG_ERROR);
return 0.0; break;
case colvarvalue::type_scalar:
return real_value; break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return rvector_value[i]; break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return quaternion_value[i]; break;
case colvarvalue::type_vector:
return vector1d_value[i]; break;
}
}
inline cvm::real & colvarvalue::operator [] (int const i)
{
switch (value_type) {
case colvarvalue::type_notset:
default:
cvm::error("Error: trying to access a colvar value "
"that is not initialized.\n", BUG_ERROR);
return real_value; break;
case colvarvalue::type_scalar:
return real_value; break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return rvector_value[i]; break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return quaternion_value[i]; break;
case colvarvalue::type_vector:
return vector1d_value[i]; break;
}
}
inline int colvarvalue::check_types(colvarvalue const &x1,
colvarvalue const &x2)
{
if (!colvarvalue::type_checking()) {
return COLVARS_OK;
}
if (x1.type() != x2.type()) {
if (((x1.type() == type_unit3vector) &&
(x2.type() == type_unit3vectorderiv)) ||
((x2.type() == type_unit3vector) &&
(x1.type() == type_unit3vectorderiv)) ||
((x1.type() == type_quaternion) &&
(x2.type() == type_quaternionderiv)) ||
((x2.type() == type_quaternion) &&
(x1.type() == type_quaternionderiv))) {
return COLVARS_OK;
} else {
cvm::error("Trying to perform an operation between two colvar "
"values with different types, \""+
colvarvalue::type_desc(x1.type())+
"\" and \""+
colvarvalue::type_desc(x2.type())+
"\".\n");
return COLVARS_ERROR;
}
}
if (x1.type() == type_vector) {
if (x1.vector1d_value.size() != x2.vector1d_value.size()) {
cvm::error("Trying to perform an operation between two vector colvar "
"values with different sizes, "+
cvm::to_str(x1.vector1d_value.size())+
" and "+
cvm::to_str(x2.vector1d_value.size())+
".\n");
return COLVARS_ERROR;
}
}
return COLVARS_OK;
}
inline int colvarvalue::check_types_assign(colvarvalue::Type const &vt1,
colvarvalue::Type const &vt2)
{
if (!colvarvalue::type_checking()) {
return COLVARS_OK;
}
if (vt1 != type_notset) {
if (((vt1 == type_unit3vector) &&
(vt2 == type_unit3vectorderiv)) ||
((vt2 == type_unit3vector) &&
(vt1 == type_unit3vectorderiv)) ||
((vt1 == type_quaternion) &&
(vt2 == type_quaternionderiv)) ||
((vt2 == type_quaternion) &&
(vt1 == type_quaternionderiv))) {
return COLVARS_OK;
} else {
if (vt1 != vt2) {
cvm::error("Trying to assign a colvar value with type \""+
type_desc(vt2)+"\" to one with type \""+
type_desc(vt1)+"\".\n");
return COLVARS_ERROR;
}
}
}
return COLVARS_OK;
}
inline colvarvalue & colvarvalue::operator = (colvarvalue const &x)
{
check_types_assign(this->type(), x.type());
value_type = x.type();
switch (this->type()) {
case colvarvalue::type_scalar:
this->real_value = x.real_value;
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
this->rvector_value = x.rvector_value;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
this->quaternion_value = x.quaternion_value;
break;
case colvarvalue::type_vector:
vector1d_value = x.vector1d_value;
elem_types = x.elem_types;
elem_indices = x.elem_indices;
elem_sizes = x.elem_sizes;
break;
case colvarvalue::type_notset:
default:
undef_op();
break;
}
return *this;
}
inline void colvarvalue::operator += (colvarvalue const &x)
{
colvarvalue::check_types(*this, x);
switch (this->type()) {
case colvarvalue::type_scalar:
this->real_value += x.real_value;
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
this->rvector_value += x.rvector_value;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
this->quaternion_value += x.quaternion_value;
break;
case colvarvalue::type_vector:
this->vector1d_value += x.vector1d_value;
break;
case colvarvalue::type_notset:
default:
undef_op();
}
}
inline void colvarvalue::operator -= (colvarvalue const &x)
{
colvarvalue::check_types(*this, x);
switch (value_type) {
case colvarvalue::type_scalar:
real_value -= x.real_value;
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
rvector_value -= x.rvector_value;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
quaternion_value -= x.quaternion_value;
break;
case colvarvalue::type_vector:
this->vector1d_value -= x.vector1d_value;
break;
case colvarvalue::type_notset:
default:
undef_op();
}
}
inline void colvarvalue::operator *= (cvm::real const &a)
{
switch (value_type) {
case colvarvalue::type_scalar:
real_value *= a;
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vectorderiv:
rvector_value *= a;
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
quaternion_value *= a;
break;
case colvarvalue::type_vector:
this->vector1d_value *= a;
break;
case colvarvalue::type_notset:
default:
undef_op();
}
}
inline void colvarvalue::operator /= (cvm::real const &a)
{
switch (value_type) {
case colvarvalue::type_scalar:
real_value /= a; break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
rvector_value /= a; break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
quaternion_value /= a; break;
case colvarvalue::type_vector:
this->vector1d_value /= a;
break;
case colvarvalue::type_notset:
default:
undef_op();
}
}
inline cvm::vector1d<cvm::real> const colvarvalue::as_vector() const
{
switch (value_type) {
case colvarvalue::type_scalar:
{
cvm::vector1d<cvm::real> v(1);
v[0] = real_value;
return v;
}
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return rvector_value.as_vector();
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return quaternion_value.as_vector();
case colvarvalue::type_vector:
return vector1d_value;
case colvarvalue::type_notset:
default:
return cvm::vector1d<cvm::real>(0);
}
}
inline cvm::real colvarvalue::norm2() const
{
switch (value_type) {
case colvarvalue::type_scalar:
return (this->real_value)*(this->real_value);
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
return (this->rvector_value).norm2();
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
return (this->quaternion_value).norm2();
case colvarvalue::type_vector:
if (elem_types.size() > 0) {
// if we have information about non-scalar types, use it
cvm::real result = 0.0;
size_t i;
for (i = 0; i < elem_types.size(); i++) {
result += (this->get_elem(i)).norm2();
}
return result;
} else {
return vector1d_value.norm2();
}
break;
case colvarvalue::type_notset:
default:
return 0.0;
}
}
inline cvm::real colvarvalue::dist2(colvarvalue const &x2) const
{
colvarvalue::check_types(*this, x2);
switch (this->type()) {
case colvarvalue::type_scalar:
return (this->real_value - x2.real_value)*(this->real_value - x2.real_value);
case colvarvalue::type_3vector:
return (this->rvector_value - x2.rvector_value).norm2();
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
// angle between (*this) and x2 is the distance
return std::acos(this->rvector_value * x2.rvector_value) * std::acos(this->rvector_value * x2.rvector_value);
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
// angle between (*this) and x2 is the distance, the quaternion
// object has it implemented internally
return this->quaternion_value.dist2(x2.quaternion_value);
case colvarvalue::type_vector:
return (this->vector1d_value - x2.vector1d_value).norm2();
case colvarvalue::type_notset:
default:
this->undef_op();
return 0.0;
};
}
#endif
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