forked from lijiext/lammps
1278 lines
42 KiB
C++
1278 lines
42 KiB
C++
// -*- c++ -*-
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// This file is part of the Collective Variables module (Colvars).
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// The original version of Colvars and its updates are located at:
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// https://github.com/colvars/colvars
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// Please update all Colvars source files before making any changes.
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// If you wish to distribute your changes, please submit them to the
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// Colvars repository at GitHub.
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#ifndef COLVARCOMP_H
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#define COLVARCOMP_H
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// Declaration of colvar::cvc base class and derived ones.
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//
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// Future cvc's could be declared on additional header files.
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// After the declaration of a new derived class, its metric
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// functions must be reimplemented as well.
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// If the new cvc has no symmetry or periodicity,
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// this can be done straightforwardly by using the macro:
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// simple_scalar_dist_functions (derived_class)
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#include <fstream>
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#include <cmath>
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#include "colvarmodule.h"
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#include "colvar.h"
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#include "colvaratoms.h"
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/// \brief Colvar component (base class); most implementations of
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/// \link cvc \endlink utilize one or more \link
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/// colvarmodule::atom \endlink or \link colvarmodule::atom_group
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/// \endlink objects to access atoms.
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///
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/// A \link cvc \endlink object (or an object of a
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/// cvc-derived class) specifies how to calculate a collective
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/// variable, its gradients and other related physical quantities
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/// which do not depend only on the numeric value (the \link colvar
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/// \endlink class already serves this purpose).
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///
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/// No restriction is set to what kind of calculation a \link
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/// cvc \endlink object performs (usually calculate an
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/// analytical function of atomic coordinates). The only constraint
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/// is that the value calculated is implemented as a \link colvarvalue
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/// \endlink object. This serves to provide a unique way to calculate
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/// scalar and non-scalar collective variables, and specify if and how
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/// they can be combined together by the parent \link colvar \endlink
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/// object.
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///
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/// <b> If you wish to implement a new collective variable component, you
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/// should write your own class by inheriting directly from \link
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/// cvc \endlink, or one of its derived classes (for instance,
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/// \link distance \endlink is frequently used, because it provides
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/// useful data and function members for any colvar based on two
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/// atom groups). The steps are: \par
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/// 1. add the name of this class under colvar.h \par
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/// 2. add a call to the parser in colvar.C, within the function colvar::colvar() \par
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/// 3. declare the class in colvarcomp.h \par
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/// 4. implement the class in one of the files colvarcomp_*.C
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///
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/// </b>
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/// The cvm::atom and cvm::atom_group classes are available to
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/// transparently communicate with the simulation program. However,
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/// they are not strictly needed, as long as all the degrees of
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/// freedom associated to the cvc are properly evolved by a simple
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/// call to e.g. apply_force().
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class colvar::cvc
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: public colvarparse, public colvardeps
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{
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public:
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/// \brief The name of the object (helps to identify this
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/// cvc instance when debugging)
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std::string name;
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/// \brief Description of the type of collective variable
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///
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/// Normally this string is set by the parent \link colvar \endlink
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/// object within its constructor, when all \link cvc \endlink
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/// objects are initialized; therefore the main "config string"
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/// constructor does not need to define it. If a \link cvc
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/// \endlink is initialized and/or a different constructor is used,
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/// this variable definition should be set within the constructor.
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std::string function_type;
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/// \brief Coefficient in the polynomial combination (default: 1.0)
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cvm::real sup_coeff;
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/// \brief Exponent in the polynomial combination (default: 1)
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int sup_np;
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/// \brief Is this a periodic component?
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bool b_periodic;
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/// \brief Period of this cvc value, (default: 0.0, non periodic)
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cvm::real period;
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/// \brief If the component is periodic, wrap around this value (default: 0.0)
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cvm::real wrap_center;
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/// \brief Constructor
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///
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/// At least one constructor which reads a string should be defined
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/// for every class inheriting from cvc \param conf Contents
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/// of the configuration file pertaining to this \link cvc
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/// \endlink
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cvc(std::string const &conf);
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/// \brief Within the constructor, make a group parse its own
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/// options from the provided configuration string
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/// Returns reference to new group
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cvm::atom_group *parse_group(std::string const &conf,
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char const *group_key,
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bool optional = false);
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/// \brief Parse options pertaining to total force calculation
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virtual int init_total_force_params(std::string const &conf);
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/// \brief After construction, set data related to dependency handling
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int setup();
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/// \brief Default constructor (used when \link cvc \endlink
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/// objects are declared within other ones)
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cvc();
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/// Destructor
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virtual ~cvc();
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/// \brief Implementation of the feature list for colvar
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static std::vector<feature *> cvc_features;
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/// \brief Implementation of the feature list accessor for colvar
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virtual std::vector<feature *> &features() {
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return cvc_features;
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}
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/// \brief Obtain data needed for the calculation for the backend
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virtual void read_data();
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/// \brief Calculate the variable
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virtual void calc_value() = 0;
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/// \brief Calculate the atomic gradients, to be reused later in
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/// order to apply forces
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virtual void calc_gradients() = 0;
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/// \brief Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component
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virtual void debug_gradients(cvm::atom_group *group);
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/// \brief Calculate the total force from the system using the
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/// inverse atomic gradients
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virtual void calc_force_invgrads();
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/// \brief Calculate the divergence of the inverse atomic gradients
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virtual void calc_Jacobian_derivative();
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/// \brief Return the previously calculated value
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colvarvalue const & value() const;
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/// \brief Return the previously calculated total force
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colvarvalue const & total_force() const;
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/// \brief Return the previously calculated divergence of the
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/// inverse atomic gradients
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colvarvalue const & Jacobian_derivative() const;
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/// \brief Apply the collective variable force, by communicating the
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/// atomic forces to the simulation program (\b Note: the \link ft
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/// \endlink member is not altered by this function)
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///
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/// Note: multiple calls to this function within the same simulation
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/// step will add the forces altogether \param cvforce The
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/// collective variable force, usually coming from the biases and
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/// eventually manipulated by the parent \link colvar \endlink
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/// object
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virtual void apply_force(colvarvalue const &cvforce) = 0;
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/// \brief Square distance between x1 and x2 (can be redefined to
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/// transparently implement constraints, symmetries and
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/// periodicities)
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///
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/// colvar::cvc::dist2() and the related functions are
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/// declared as "const" functions, but not "static", because
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/// additional parameters defining the metrics (e.g. the
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/// periodicity) may be specific to each colvar::cvc object.
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///
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/// If symmetries or periodicities are present, the
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/// colvar::cvc::dist2() should be redefined to return the
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/// "closest distance" value and colvar::cvc::dist2_lgrad(),
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/// colvar::cvc::dist2_rgrad() to return its gradients.
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///
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/// If constraints are present (and not already implemented by any
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/// of the \link colvarvalue \endlink types), the
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/// colvar::cvc::dist2_lgrad() and
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/// colvar::cvc::dist2_rgrad() functions should be redefined
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/// to provide a gradient which is compatible with the constraint,
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/// i.e. already deprived of its component normal to the constraint
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/// hypersurface.
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///
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/// Finally, another useful application, if you are performing very
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/// many operations with these functions, could be to override the
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/// \link colvarvalue \endlink member functions and access directly
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/// its member data. For instance: to define dist2(x1,x2) as
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/// (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in
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/// case of a scalar \link colvarvalue \endlink type.
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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/// \brief Gradient(with respect to x1) of the square distance (can
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/// be redefined to transparently implement constraints, symmetries
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/// and periodicities)
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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/// \brief Gradient(with respect to x2) of the square distance (can
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/// be redefined to transparently implement constraints, symmetries
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/// and periodicities)
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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/// \brief Wrapp value (for periodic/symmetric cvcs)
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virtual void wrap(colvarvalue &x) const;
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/// \brief Pointers to all atom groups, to let colvars collect info
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/// e.g. atomic gradients
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std::vector<cvm::atom_group *> atom_groups;
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/// \brief Whether or not this CVC will be computed in parallel whenever possible
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bool b_try_scalable;
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protected:
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/// \brief Cached value
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colvarvalue x;
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/// \brief Value at the previous step
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colvarvalue x_old;
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/// \brief Calculated total force (\b Note: this is calculated from
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/// the total atomic forces read from the program, subtracting fromt
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/// the "internal" forces of the system the "external" forces from
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/// the colvar biases)
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colvarvalue ft;
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/// \brief Calculated Jacobian derivative (divergence of the inverse
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/// gradients): serves to calculate the phase space correction
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colvarvalue jd;
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};
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inline colvarvalue const & colvar::cvc::value() const
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{
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return x;
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}
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inline colvarvalue const & colvar::cvc::total_force() const
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{
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return ft;
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}
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inline colvarvalue const & colvar::cvc::Jacobian_derivative() const
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{
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return jd;
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}
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/// \brief Colvar component: distance between the centers of mass of
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/// two groups (colvarvalue::type_scalar type, range [0:*))
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class colvar::distance
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: public colvar::cvc
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{
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protected:
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/// First atom group
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cvm::atom_group *group1;
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/// Second atom group
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cvm::atom_group *group2;
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/// Vector distance, cached to be recycled
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cvm::rvector dist_v;
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/// Use absolute positions, ignoring PBCs when present
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bool b_no_PBC;
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public:
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distance(std::string const &conf);
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distance();
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virtual ~distance() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void calc_force_invgrads();
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virtual void calc_Jacobian_derivative();
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virtual void apply_force(colvarvalue const &force);
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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};
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// \brief Colvar component: distance vector between centers of mass
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// of two groups (\link colvarvalue::type_3vector \endlink type,
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// range (-*:*)x(-*:*)x(-*:*))
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class colvar::distance_vec
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: public colvar::distance
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{
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public:
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distance_vec(std::string const &conf);
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distance_vec();
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virtual ~distance_vec() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void apply_force(colvarvalue const &force);
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/// Redefined to handle the box periodicity
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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/// Redefined to handle the box periodicity
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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/// Redefined to handle the box periodicity
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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};
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/// \brief Colvar component: distance unit vector (direction) between
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/// centers of mass of two groups (colvarvalue::type_unit3vector type,
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/// range [-1:1]x[-1:1]x[-1:1])
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class colvar::distance_dir
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: public colvar::distance
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{
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public:
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distance_dir(std::string const &conf);
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distance_dir();
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virtual ~distance_dir() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void apply_force(colvarvalue const &force);
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};
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/// \brief Colvar component: projection of the distance vector along
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/// an axis(colvarvalue::type_scalar type, range (-*:*))
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class colvar::distance_z
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: public colvar::cvc
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{
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protected:
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/// Main atom group
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cvm::atom_group *main;
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/// Reference atom group
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cvm::atom_group *ref1;
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/// Optional, second ref atom group
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cvm::atom_group *ref2;
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/// Use absolute positions, ignoring PBCs when present
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bool b_no_PBC;
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/// Vector on which the distance vector is projected
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cvm::rvector axis;
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/// Norm of the axis
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cvm::real axis_norm;
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/// Vector distance, cached to be recycled
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cvm::rvector dist_v;
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/// Flag: using a fixed axis vector?
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bool fixed_axis;
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public:
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distance_z(std::string const &conf);
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distance_z();
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virtual ~distance_z() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void calc_force_invgrads();
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virtual void calc_Jacobian_derivative();
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virtual void apply_force(colvarvalue const &force);
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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/// \brief Redefined to make use of the user-provided period
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virtual void wrap(colvarvalue &x) const;
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};
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/// \brief Colvar component: projection of the distance vector on a
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/// plane (colvarvalue::type_scalar type, range [0:*))
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class colvar::distance_xy
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: public colvar::distance_z
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{
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protected:
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/// Components of the distance vector orthogonal to the axis
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cvm::rvector dist_v_ortho;
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/// Vector distances
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cvm::rvector v12, v13;
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public:
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distance_xy(std::string const &conf);
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distance_xy();
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virtual ~distance_xy() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void calc_force_invgrads();
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virtual void calc_Jacobian_derivative();
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virtual void apply_force(colvarvalue const &force);
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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};
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/// \brief Colvar component: average distance between two groups of atoms, weighted as the sixth power,
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/// as in NMR refinements(colvarvalue::type_scalar type, range (0:*))
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class colvar::distance_inv
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: public colvar::distance
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{
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protected:
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/// Components of the distance vector orthogonal to the axis
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int exponent;
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public:
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distance_inv(std::string const &conf);
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distance_inv();
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virtual ~distance_inv() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void apply_force(colvarvalue const &force);
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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};
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/// \brief Colvar component: N1xN2 vector of pairwise distances
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/// (colvarvalue::type_vector type, range (0:*) for each component)
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class colvar::distance_pairs
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: public colvar::cvc
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{
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protected:
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/// First atom group
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cvm::atom_group *group1;
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/// Second atom group
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cvm::atom_group *group2;
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/// Use absolute positions, ignoring PBCs when present
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bool b_no_PBC;
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public:
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distance_pairs(std::string const &conf);
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distance_pairs();
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virtual ~distance_pairs() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void apply_force(colvarvalue const &force);
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};
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/// \brief Colvar component: Radius of gyration of an atom group
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/// (colvarvalue::type_scalar type, range [0:*))
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class colvar::gyration
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: public colvar::cvc
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{
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protected:
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/// Atoms involved
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cvm::atom_group *atoms;
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public:
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/// Constructor
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gyration(std::string const &conf);
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gyration();
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virtual ~gyration() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void calc_force_invgrads();
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virtual void calc_Jacobian_derivative();
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virtual void apply_force(colvarvalue const &force);
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
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colvarvalue const &x2) const;
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};
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/// \brief Colvar component: moment of inertia of an atom group
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/// (colvarvalue::type_scalar type, range [0:*))
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class colvar::inertia
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: public colvar::gyration
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{
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public:
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/// Constructor
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inertia(std::string const &conf);
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inertia();
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virtual ~inertia() {}
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virtual void calc_value();
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virtual void calc_gradients();
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virtual void apply_force(colvarvalue const &force);
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virtual cvm::real dist2(colvarvalue const &x1,
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colvarvalue const &x2) const;
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virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
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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 ~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 ~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 ~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 ~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 ~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 ~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 ~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: coordination number between two groups
|
|
/// (colvarvalue::type_scalar type, range [0:N1*N2])
|
|
class colvar::groupcoordnum
|
|
: public colvar::distance
|
|
{
|
|
protected:
|
|
/// \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;
|
|
public:
|
|
/// Constructor
|
|
groupcoordnum(std::string const &conf);
|
|
groupcoordnum();
|
|
virtual ~groupcoordnum() {}
|
|
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: 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 ~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;
|
|
};
|
|
|
|
|
|
|
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/// \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
|
|
{
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|
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 ~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 ~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 ~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 ~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 ~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 ~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 ~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) \
|
|
\
|
|
\
|
|
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); \
|
|
} \
|
|
\
|
|
\
|
|
colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1, \
|
|
colvarvalue const &x2) const \
|
|
{ \
|
|
return 2.0 * (x1.real_value - x2.real_value); \
|
|
} \
|
|
\
|
|
\
|
|
colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1, \
|
|
colvarvalue const &x2) const \
|
|
{ \
|
|
return this->dist2_lgrad(x2, x1); \
|
|
} \
|
|
\
|
|
|
|
#endif
|