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lammps/lib/colvars/colvarcomp.h
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colvarcomp.h
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// -*- c++ -*-
#ifndef COLVARCOMP_H
#define COLVARCOMP_H
// Declaration of colvar::cvc base class and derived ones.
//
// Future cvc's could be declared on additional header files.
// After the declaration of a new derived class, its metric
// functions must be reimplemented as well.
// If the new cvc has no symmetry or periodicity,
// this can be done straightforwardly by using the macro:
// simple_scalar_dist_functions (derived_class)
#include <fstream>
#include <cmath>
#include "colvarmodule.h"
#include "colvar.h"
#include "colvaratoms.h"
/// \brief Colvar component (base class); most implementations of
/// \link cvc \endlink utilize one or more \link
/// colvarmodule::atom \endlink or \link colvarmodule::atom_group
/// \endlink objects to access atoms.
///
/// A \link cvc \endlink object (or an object of a
/// cvc-derived class) specifies how to calculate a collective
/// variable, its gradients and other related physical quantities
/// which do not depend only on the numeric value (the \link colvar
/// \endlink class already serves this purpose).
///
/// No restriction is set to what kind of calculation a \link
/// cvc \endlink object performs (usually calculate an
/// analytical function of atomic coordinates). The only constraint
/// is that the value calculated is implemented as a \link colvarvalue
/// \endlink object. This serves to provide a unique way to calculate
/// scalar and non-scalar collective variables, and specify if and how
/// they can be combined together by the parent \link colvar \endlink
/// object.
///
/// <b> If you wish to implement a new collective variable component, you
/// should write your own class by inheriting directly from \link
/// cvc \endlink, or one of its derived classes (for instance,
/// \link distance \endlink is frequently used, because it provides
/// useful data and function members for any colvar based on two
/// atom groups). The steps are: \par
/// 1. add the name of this class under colvar.h \par
/// 2. add a call to the parser in colvar.C, within the function colvar::colvar() \par
/// 3. declare the class in colvarcomp.h \par
/// 4. implement the class in one of the files colvarcomp_*.C
///
/// </b>
/// The cvm::atom and cvm::atom_group classes are available to
/// transparently communicate with the simulation program. However,
/// they are not strictly needed, as long as all the degrees of
/// freedom associated to the cvc are properly evolved by a simple
/// call to e.g. apply_force().
class colvar::cvc
: public colvarparse, public colvardeps
{
public:
/// \brief The name of the object (helps to identify this
/// cvc instance when debugging)
std::string name;
/// \brief Description of the type of collective variable
///
/// Normally this string is set by the parent \link colvar \endlink
/// object within its constructor, when all \link cvc \endlink
/// objects are initialized; therefore the main "config string"
/// constructor does not need to define it. If a \link cvc
/// \endlink is initialized and/or a different constructor is used,
/// this variable definition should be set within the constructor.
std::string function_type;
/// \brief Coefficient in the polynomial combination (default: 1.0)
cvm::real sup_coeff;
/// \brief Exponent in the polynomial combination (default: 1)
int sup_np;
/// \brief Is this a periodic component?
bool b_periodic;
/// \brief Period of this cvc value, (default: 0.0, non periodic)
cvm::real period;
/// \brief If the component is periodic, wrap around this value (default: 0.0)
cvm::real wrap_center;
/// \brief Constructor
///
/// At least one constructor which reads a string should be defined
/// for every class inheriting from cvc \param conf Contents
/// of the configuration file pertaining to this \link cvc
/// \endlink
cvc(std::string const &conf);
/// \brief Within the constructor, make a group parse its own
/// options from the provided configuration string
/// Returns reference to new group
cvm::atom_group *parse_group(std::string const &conf,
char const *group_key,
bool optional = false);
/// \brief After construction, set data related to dependency handling
int setup();
/// \brief Default constructor (used when \link cvc \endlink
/// objects are declared within other ones)
cvc();
/// Destructor
virtual ~cvc();
/// \brief Implementation of the feature list for colvar
static std::vector<feature *> cvc_features;
/// \brief Implementation of the feature list accessor for colvar
virtual std::vector<feature *> &features() {
return cvc_features;
}
/// \brief Obtain data needed for the calculation for the backend
void read_data();
/// \brief Calculate the variable
virtual void calc_value() = 0;
/// \brief Calculate the atomic gradients, to be reused later in
/// order to apply forces
virtual void calc_gradients() = 0;
/// \brief Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component
virtual void debug_gradients(cvm::atom_group *group);
/// \brief Calculate the total force from the system using the
/// inverse atomic gradients
virtual void calc_force_invgrads();
/// \brief Calculate the divergence of the inverse atomic gradients
virtual void calc_Jacobian_derivative();
/// \brief Return the previously calculated value
virtual colvarvalue const & value() const;
// /// \brief Return const pointer to the previously calculated value
// virtual const colvarvalue *p_value() const;
/// \brief Return the previously calculated total force
virtual colvarvalue const & total_force() const;
/// \brief Return the previously calculated divergence of the
/// inverse atomic gradients
virtual colvarvalue const & Jacobian_derivative() const;
/// \brief Apply the collective variable force, by communicating the
/// atomic forces to the simulation program (\b Note: the \link ft
/// \endlink member is not altered by this function)
///
/// Note: multiple calls to this function within the same simulation
/// step will add the forces altogether \param cvforce The
/// collective variable force, usually coming from the biases and
/// eventually manipulated by the parent \link colvar \endlink
/// object
virtual void apply_force(colvarvalue const &cvforce) = 0;
/// \brief 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 \link colvarvalue \endlink 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
/// \link colvarvalue \endlink 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 \link colvarvalue \endlink type.
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Gradient(with respect to x1) of the square distance (can
/// be redefined to transparently implement constraints, symmetries
/// and periodicities)
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Gradient(with respect to x2) 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;
/// \brief Wrapp value (for periodic/symmetric cvcs)
virtual void wrap(colvarvalue &x) const;
/// \brief Pointers to all atom groups, to let colvars collect info
/// e.g. atomic gradients
std::vector<cvm::atom_group *> atom_groups;
/// \brief Whether or not this CVC will be computed in parallel whenever possible
bool b_try_scalable;
protected:
/// \brief Cached value
colvarvalue x;
/// \brief Value at the previous step
colvarvalue x_old;
/// \brief Calculated total force (\b 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 ft;
/// \brief Calculated Jacobian derivative (divergence of the inverse
/// gradients): serves to calculate the phase space correction
colvarvalue jd;
};
inline colvarvalue const & colvar::cvc::value() const
{
return x;
}
// inline const colvarvalue * colvar::cvc::p_value() const
// {
// return &x;
// }
inline colvarvalue const & colvar::cvc::total_force() const
{
return ft;
}
inline colvarvalue const & colvar::cvc::Jacobian_derivative() const
{
return jd;
}
inline cvm::real colvar::cvc::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.dist2(x2);
}
inline colvarvalue colvar::cvc::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.dist2_grad(x2);
}
inline colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x2.dist2_grad(x1);
}
inline void colvar::cvc::wrap(colvarvalue &x) const
{
return;
}
/// \brief Colvar component: distance between the centers of mass of
/// two groups (colvarvalue::type_scalar type, range [0:*))
class colvar::distance
: public colvar::cvc
{
protected:
/// First atom group
cvm::atom_group *group1;
/// Second atom group
cvm::atom_group *group2;
/// Vector distance, cached to be recycled
cvm::rvector dist_v;
/// Use absolute positions, ignoring PBCs when present
bool b_no_PBC;
/// Compute total force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
public:
distance(std::string const &conf);
distance();
virtual inline ~distance() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
// \brief Colvar component: distance vector between centers of mass
// of two groups (\link colvarvalue::type_3vector \endlink type,
// range (-*:*)x(-*:*)x(-*:*))
class colvar::distance_vec
: public colvar::distance
{
public:
distance_vec(std::string const &conf);
distance_vec();
virtual inline ~distance_vec() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
/// Redefined to handle the box periodicity
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the box periodicity
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the box periodicity
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: distance unit vector (direction) between
/// centers of mass of two groups (colvarvalue::type_unit3vector type,
/// range [-1:1]x[-1:1]x[-1:1])
class colvar::distance_dir
: public colvar::distance
{
public:
distance_dir(std::string const &conf);
distance_dir();
virtual inline ~distance_dir() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: projection of the distance vector along
/// an axis(colvarvalue::type_scalar type, range (-*:*))
class colvar::distance_z
: public colvar::cvc
{
protected:
/// Main atom group
cvm::atom_group *main;
/// Reference atom group
cvm::atom_group *ref1;
/// Optional, second ref atom group
cvm::atom_group *ref2;
/// Use absolute positions, ignoring PBCs when present
bool b_no_PBC;
/// Compute total force on one site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
/// Vector on which the distance vector is projected
cvm::rvector axis;
/// Norm of the axis
cvm::real axis_norm;
/// Vector distance, cached to be recycled
cvm::rvector dist_v;
/// Flag: using a fixed axis vector?
bool fixed_axis;
public:
distance_z(std::string const &conf);
distance_z();
virtual inline ~distance_z() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Redefined to make use of the user-provided period
virtual void wrap(colvarvalue &x) const;
};
/// \brief Colvar component: projection of the distance vector on a
/// plane (colvarvalue::type_scalar type, range [0:*))
class colvar::distance_xy
: public colvar::distance_z
{
protected:
/// Components of the distance vector orthogonal to the axis
cvm::rvector dist_v_ortho;
/// Vector distances
cvm::rvector v12, v13;
public:
distance_xy(std::string const &conf);
distance_xy();
virtual inline ~distance_xy() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: average distance between two groups of atoms, weighted as the sixth power,
/// as in NMR refinements(colvarvalue::type_scalar type, range (0:*))
class colvar::distance_inv
: public colvar::distance
{
protected:
/// Components of the distance vector orthogonal to the axis
int exponent;
public:
distance_inv(std::string const &conf);
distance_inv();
virtual inline ~distance_inv() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: N1xN2 vector of pairwise distances
/// (colvarvalue::type_vector type, range (0:*) for each component)
class colvar::distance_pairs
: public colvar::cvc
{
protected:
/// First atom group
cvm::atom_group *group1;
/// Second atom group
cvm::atom_group *group2;
/// Use absolute positions, ignoring PBCs when present
bool b_no_PBC;
public:
distance_pairs(std::string const &conf);
distance_pairs();
virtual inline ~distance_pairs() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: Radius of gyration of an atom group
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::gyration
: public colvar::cvc
{
protected:
/// Atoms involved
cvm::atom_group *atoms;
public:
/// Constructor
gyration(std::string const &conf);
gyration();
virtual inline ~gyration() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: moment of inertia of an atom group
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::inertia
: public colvar::gyration
{
public:
/// Constructor
inertia(std::string const &conf);
inertia();
virtual inline ~inertia() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: moment of inertia of an atom group
/// around a user-defined axis (colvarvalue::type_scalar type, range [0:*))
class colvar::inertia_z
: public colvar::inertia
{
protected:
/// Vector on which the inertia tensor is projected
cvm::rvector axis;
public:
/// Constructor
inertia_z(std::string const &conf);
inertia_z();
virtual inline ~inertia_z() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: projection of 3N coordinates onto an
/// eigenvector(colvarvalue::type_scalar type, range (-*:*))
class colvar::eigenvector
: public colvar::cvc
{
protected:
/// Atom group
cvm::atom_group * atoms;
/// Reference coordinates
std::vector<cvm::atom_pos> ref_pos;
/// Geometric center of the reference coordinates
cvm::atom_pos ref_pos_center;
/// Eigenvector (of a normal or essential mode): will always have zero center
std::vector<cvm::rvector> eigenvec;
/// Inverse square norm of the eigenvector
cvm::real eigenvec_invnorm2;
public:
/// Constructor
eigenvector(std::string const &conf);
virtual inline ~eigenvector() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: angle between the centers of mass of
/// three groups (colvarvalue::type_scalar type, range [0:PI])
class colvar::angle
: public colvar::cvc
{
protected:
/// Atom group
cvm::atom_group *group1;
/// Atom group
cvm::atom_group *group2;
/// Atom group
cvm::atom_group *group3;
/// Inter site vectors
cvm::rvector r21, r23;
/// Inter site vector norms
cvm::real r21l, r23l;
/// Derivatives wrt group centers of mass
cvm::rvector dxdr1, dxdr3;
/// Compute total force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
/// (or to allow dummy atoms)
bool b_1site_force;
public:
/// Initialize by parsing the configuration
angle(std::string const &conf);
/// \brief Initialize the three groups after three atoms
angle(cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3);
angle();
virtual inline ~angle() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: angle between the dipole of a molecule and an axis
/// formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI])
class colvar::dipole_angle
: public colvar::cvc
{
protected:
/// Dipole atom group
cvm::atom_group *group1;
/// Atom group
cvm::atom_group *group2;
/// Atom group
cvm::atom_group *group3;
/// Inter site vectors
cvm::rvector r21, r23;
/// Inter site vector norms
cvm::real r21l, r23l;
/// Derivatives wrt group centers of mass
cvm::rvector dxdr1, dxdr3;
/// Compute total force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
/// (or to allow dummy atoms)
bool b_1site_force;
public:
/// Initialize by parsing the configuration
dipole_angle (std::string const &conf);
/// \brief Initialize the three groups after three atoms
dipole_angle (cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3);
dipole_angle();
virtual inline ~dipole_angle() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force (colvarvalue const &force);
virtual cvm::real dist2 (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: dihedral between the centers of mass of
/// four groups (colvarvalue::type_scalar type, range [-PI:PI])
class colvar::dihedral
: public colvar::cvc
{
protected:
/// Atom group
cvm::atom_group *group1;
/// Atom group
cvm::atom_group *group2;
/// Atom group
cvm::atom_group *group3;
/// Atom group
cvm::atom_group *group4;
/// Inter site vectors
cvm::rvector r12, r23, r34;
/// \brief Compute total force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
public:
/// Initialize by parsing the configuration
dihedral(std::string const &conf);
/// \brief Initialize the four groups after four atoms
dihedral(cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3, cvm::atom const &a4);
dihedral();
virtual inline ~dihedral() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
/// Redefined to handle the 2*PI periodicity
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual void wrap(colvarvalue &x) const;
};
/// \brief Colvar component: coordination number between two groups
/// (colvarvalue::type_scalar type, range [0:N1*N2])
class colvar::coordnum
: public colvar::cvc
{
protected:
/// First atom group
cvm::atom_group *group1;
/// Second atom group
cvm::atom_group *group2;
/// \brief "Cutoff" for isotropic calculation (default)
cvm::real r0;
/// \brief "Cutoff vector" for anisotropic calculation
cvm::rvector r0_vec;
/// \brief Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be
/// used
bool b_anisotropic;
/// Integer exponent of the function numerator
int en;
/// Integer exponent of the function denominator
int ed;
/// \brief If true, group2 will be treated as a single atom
/// (default: loop over all pairs of atoms in group1 and group2)
bool b_group2_center_only;
public:
/// Constructor
coordnum(std::string const &conf);
coordnum();
virtual inline ~coordnum() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |A1-A2|/r0 \param r0 "cutoff" for the
/// coordination number \param exp_num \i n exponent \param exp_den
/// \i m exponent \param A1 atom \param A2 atom
static cvm::real switching_function(cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |(A1-A2)*(r0_vec)^-|1 \param r0_vec
/// vector of different cutoffs in the three directions \param
/// exp_num \i n exponent \param exp_den \i m exponent \param A1
/// atom \param A2 atom
static cvm::real switching_function(cvm::rvector const &r0_vec,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: self-coordination number within a group
/// (colvarvalue::type_scalar type, range [0:N*(N-1)/2])
class colvar::selfcoordnum
: public colvar::cvc
{
protected:
/// First atom group
cvm::atom_group *group1;
/// \brief "Cutoff" for isotropic calculation (default)
cvm::real r0;
/// Integer exponent of the function numerator
int en;
/// Integer exponent of the function denominator
int ed;
public:
/// Constructor
selfcoordnum(std::string const &conf);
selfcoordnum();
virtual inline ~selfcoordnum() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |A1-A2|/r0 \param r0 "cutoff" for the
/// coordination number \param exp_num \i n exponent \param exp_den
/// \i m exponent \param A1 atom \param A2 atom
static cvm::real switching_function(cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: hydrogen bond, defined as the product of
/// a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol))
/// (colvarvalue::type_scalar type, range [0:1])
class colvar::h_bond
: public colvar::cvc
{
protected:
/// \brief "Cutoff" distance between acceptor and donor
cvm::real r0;
/// Integer exponent of the function numerator
int en;
/// Integer exponent of the function denominator
int ed;
public:
h_bond(std::string const &conf);
/// Constructor for atoms already allocated
h_bond(cvm::atom const &acceptor,
cvm::atom const &donor,
cvm::real r0, int en, int ed);
h_bond();
virtual ~h_bond();
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: alpha helix content of a contiguous
/// segment of 5 or more residues, implemented as a sum of phi/psi
/// dihedral angles and hydrogen bonds (colvarvalue::type_scalar type,
/// range [0:1])
// class colvar::alpha_dihedrals
// : public colvar::cvc
// {
// protected:
// /// Alpha-helical reference phi value
// cvm::real phi_ref;
// /// Alpha-helical reference psi value
// cvm::real psi_ref;
// /// List of phi dihedral angles
// std::vector<dihedral *> phi;
// /// List of psi dihedral angles
// std::vector<dihedral *> psi;
// /// List of hydrogen bonds
// std::vector<h_bond *> hb;
// public:
// alpha_dihedrals (std::string const &conf);
// alpha_dihedrals();
// virtual inline ~alpha_dihedrals() {}
// virtual void calc_value();
// virtual void calc_gradients();
// virtual void apply_force (colvarvalue const &force);
// virtual cvm::real dist2 (colvarvalue const &x1,
// colvarvalue const &x2) const;
// virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
// colvarvalue const &x2) const;
// virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
// colvarvalue const &x2) const;
// };
/// \brief Colvar component: alpha helix content of a contiguous
/// segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca
/// angles and hydrogen bonds (colvarvalue::type_scalar type, range
/// [0:1])
class colvar::alpha_angles
: public colvar::cvc
{
protected:
/// Reference Calpha-Calpha angle (default: 88 degrees)
cvm::real theta_ref;
/// Tolerance on the Calpha-Calpha angle
cvm::real theta_tol;
/// List of Calpha-Calpha angles
std::vector<angle *> theta;
/// List of hydrogen bonds
std::vector<h_bond *> hb;
/// Contribution of the hb terms
cvm::real hb_coeff;
public:
alpha_angles(std::string const &conf);
alpha_angles();
virtual ~alpha_angles();
void calc_value();
void calc_gradients();
void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: dihedPC
/// Projection of the config onto a dihedral principal component
/// See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007)
/// Based on a set of 'dihedral' cvcs
class colvar::dihedPC
: public colvar::cvc
{
protected:
std::vector<dihedral *> theta;
std::vector<cvm::real> coeffs;
public:
dihedPC(std::string const &conf);
dihedPC();
virtual ~dihedPC();
void calc_value();
void calc_gradients();
void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: orientation in space of an atom group,
/// with respect to a set of reference coordinates
/// (colvarvalue::type_quaternion type, range
/// [-1:1]x[-1:1]x[-1:1]x[-1:1])
class colvar::orientation
: public colvar::cvc
{
protected:
/// Atom group
cvm::atom_group * atoms;
/// Center of geometry of the group
cvm::atom_pos atoms_cog;
/// Reference coordinates
std::vector<cvm::atom_pos> ref_pos;
/// Rotation object
cvm::rotation rot;
/// \brief This is used to remove jumps in the sign of the
/// quaternion, which may be annoying in the colvars trajectory
cvm::quaternion ref_quat;
public:
orientation(std::string const &conf);
orientation();
virtual inline ~orientation() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: angle of rotation with respect to a set
/// of reference coordinates (colvarvalue::type_scalar type, range
/// [0:PI))
class colvar::orientation_angle
: public colvar::orientation
{
public:
orientation_angle(std::string const &conf);
orientation_angle();
virtual inline ~orientation_angle() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: cosine of the angle of rotation with respect to a set
/// of reference coordinates (colvarvalue::type_scalar type, range
/// [-1:1])
class colvar::orientation_proj
: public colvar::orientation
{
public:
orientation_proj(std::string const &conf);
orientation_proj();
virtual inline ~orientation_proj() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: projection of the orientation vector onto
/// a predefined axis (colvarvalue::type_scalar type, range [-1:1])
class colvar::tilt
: public colvar::orientation
{
protected:
cvm::rvector axis;
public:
tilt(std::string const &conf);
tilt();
virtual inline ~tilt() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: angle of rotation around a predefined
/// axis (colvarvalue::type_scalar type, range [-PI:PI])
class colvar::spin_angle
: public colvar::orientation
{
protected:
cvm::rvector axis;
public:
spin_angle(std::string const &conf);
spin_angle();
virtual inline ~spin_angle() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
/// Redefined to handle the 2*PI periodicity
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual void wrap(colvarvalue &x) const;
};
/// \brief Colvar component: root mean square deviation (RMSD) of a
/// group with respect to a set of reference coordinates; uses \link
/// colvar::orientation \endlink to calculate the rotation matrix
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::rmsd
: public colvar::cvc
{
protected:
/// Atom group
cvm::atom_group *atoms;
/// Reference coordinates (for RMSD calculation only)
std::vector<cvm::atom_pos> ref_pos;
public:
/// Constructor
rmsd(std::string const &conf);
virtual inline ~rmsd() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
virtual void apply_force(colvarvalue const &force);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
};
// \brief Colvar component: flat vector of Cartesian coordinates
// Mostly useful to compute scripted colvar values
class colvar::cartesian
: public colvar::cvc
{
protected:
/// Atom group
cvm::atom_group *atoms;
/// Which Cartesian coordinates to include
std::vector<size_t> axes;
public:
cartesian(std::string const &conf);
cartesian();
virtual inline ~cartesian() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
};
// metrics functions for cvc implementations
// simple definitions of the distance functions; these are useful only
// for optimization (the type check performed in the default
// colvarcomp functions is skipped)
// definitions assuming the scalar type
#define simple_scalar_dist_functions(TYPE) \
\
inline cvm::real colvar::TYPE::dist2(colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return 2.0 * (x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad(x2, x1); \
} \
\
simple_scalar_dist_functions(distance)
// NOTE: distance_z has explicit functions, see below
simple_scalar_dist_functions(distance_xy)
simple_scalar_dist_functions(distance_inv)
simple_scalar_dist_functions(angle)
simple_scalar_dist_functions(dipole_angle)
simple_scalar_dist_functions(coordnum)
simple_scalar_dist_functions(selfcoordnum)
simple_scalar_dist_functions(h_bond)
simple_scalar_dist_functions(gyration)
simple_scalar_dist_functions(inertia)
simple_scalar_dist_functions(inertia_z)
simple_scalar_dist_functions(rmsd)
simple_scalar_dist_functions(orientation_angle)
simple_scalar_dist_functions(orientation_proj)
simple_scalar_dist_functions(tilt)
simple_scalar_dist_functions(eigenvector)
// simple_scalar_dist_functions (alpha_dihedrals)
simple_scalar_dist_functions(alpha_angles)
simple_scalar_dist_functions(dihedPC)
// metrics functions for cvc implementations with a periodicity
inline cvm::real colvar::dihedral::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return diff * diff;
}
inline colvarvalue colvar::dihedral::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return 2.0 * diff;
}
inline colvarvalue colvar::dihedral::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return (-2.0) * diff;
}
inline void colvar::dihedral::wrap(colvarvalue &x) const
{
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
return;
}
inline cvm::real colvar::spin_angle::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return diff * diff;
}
inline colvarvalue colvar::spin_angle::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return 2.0 * diff;
}
inline colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
return (-2.0) * diff;
}
inline void colvar::spin_angle::wrap(colvarvalue &x) const
{
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
return;
}
// Projected distance
// Differences should always be wrapped around 0 (ignoring wrap_center)
inline cvm::real colvar::distance_z::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
if (period != 0.0) {
cvm::real shift = std::floor(diff/period + 0.5);
diff -= shift * period;
}
return diff * diff;
}
inline colvarvalue colvar::distance_z::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
if (period != 0.0) {
cvm::real shift = std::floor(diff/period + 0.5);
diff -= shift * period;
}
return 2.0 * diff;
}
inline colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::real diff = x1.real_value - x2.real_value;
if (period != 0.0) {
cvm::real shift = std::floor(diff/period + 0.5);
diff -= shift * period;
}
return (-2.0) * diff;
}
inline void colvar::distance_z::wrap(colvarvalue &x) const
{
if (! this->b_periodic) {
// don't wrap if the period has not been set
return;
}
cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5);
x.real_value -= shift * period;
return;
}
// distance between three dimensional vectors
//
// TODO apply PBC to distance_vec
// Note: differences should be centered around (0, 0, 0)!
inline cvm::real colvar::distance_vec::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
return cvm::position_dist2(x1.rvector_value, x2.rvector_value);
}
inline colvarvalue colvar::distance_vec::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
}
inline colvarvalue colvar::distance_vec::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
}
inline cvm::real colvar::distance_dir::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
return (x1.rvector_value - x2.rvector_value).norm2();
}
inline colvarvalue colvar::distance_dir::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return colvarvalue((x1.rvector_value - x2.rvector_value), colvarvalue::type_unit3vector);
}
inline colvarvalue colvar::distance_dir::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return colvarvalue((x2.rvector_value - x1.rvector_value), colvarvalue::type_unit3vector);
}
inline cvm::real colvar::distance_pairs::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
return (x1.vector1d_value - x2.vector1d_value).norm2();
}
inline colvarvalue colvar::distance_pairs::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return colvarvalue((x1.vector1d_value - x2.vector1d_value), colvarvalue::type_vector);
}
inline colvarvalue colvar::distance_pairs::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return colvarvalue((x2.vector1d_value - x1.vector1d_value), colvarvalue::type_vector);
}
// distance between quaternions
inline cvm::real colvar::orientation::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.quaternion_value.dist2(x2);
}
inline colvarvalue colvar::orientation::dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x1.quaternion_value.dist2_grad(x2);
}
inline colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const
{
return x2.quaternion_value.dist2_grad(x1);
}
#endif
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