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lammps/lib/colvars/colvar.h
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colvar.h
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// -*- c++ -*-
#ifndef COLVAR_H
#define COLVAR_H
#include <iostream>
#include <iomanip>
#include <cmath>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvardeps.h"
/// \brief A collective variable (main class); to be defined, it needs
/// at least one object of a derived class of colvar::cvc; it
/// calculates and returns a \link colvarvalue \endlink object
///
/// This class parses the configuration, defines the behaviour and
/// stores the value (\link colvar::x \endlink) and all related data
/// of a collective variable. How the value is calculated is defined
/// in \link colvar::cvc \endlink and its derived classes. The
/// \link colvar \endlink object contains pointers to multiple \link
/// colvar::cvc \endlink derived objects, which can be combined
/// together into one collective variable. This makes possible to
/// implement new collective variables at runtime based on the
/// existing ones. Currently, this possibility is limited to a
/// polynomial, using the coefficients cvc::sup_coeff and the
/// exponents cvc::sup_np. In case of non-scalar variables,
/// only exponents equal to 1 are accepted.
///
/// Please note that most of its members are \link colvarvalue
/// \endlink objects, i.e. they can handle different data types
/// together, and must all be set to the same type of colvar::value()
/// before using them together in assignments or other operations; this is usually done
/// automatically in the constructor. If you add a new member of
/// \link colvarvalue \endlink type, you should also add its
/// initialization line in the \link colvar \endlink constructor.
class colvar : public colvarparse, public cvm::deps {
public:
/// Name
std::string name;
/// \brief Current value (previously set by calc() or by read_traj())
colvarvalue const & value() const;
/// \brief Current actual value (not extended DOF)
colvarvalue const & actual_value() const;
/// \brief Current velocity (previously set by calc() or by read_traj())
colvarvalue const & velocity() const;
/// \brief Current system force (previously obtained from calc() or
/// read_traj()). Note: this is calculated using the atomic forces
/// from the last simulation step.
///
/// Total atom forces are read from the MD program, the total force
/// acting on the collective variable is calculated summing those
/// from all colvar components, the bias and walls forces are
/// subtracted.
colvarvalue const & system_force() const;
/// \brief Typical fluctuation amplitude for this collective
/// variable (e.g. local width of a free energy basin)
///
/// In metadynamics calculations, \link colvarbias_meta \endlink,
/// this value is used to calculate the width of a gaussian. In ABF
/// calculations, \link colvarbias_abf \endlink, it is used to
/// calculate the grid spacing in the direction of this collective
/// variable.
cvm::real width;
/// \brief Implementation of the feature list for colvar
static std::vector<feature *> cv_features;
/// \brief Implementation of the feature list accessor for colvar
std::vector<feature *> &features() {
return cv_features;
}
int refresh_deps();
/// List of biases that depend on this colvar
std::vector<colvarbias *> biases;
protected:
/*
extended:
H = H_{0} + \sum_{i} 1/2*\lambda*(S_i(x(t))-s_i(t))^2 \\
+ \sum_{i} 1/2*m_i*(ds_i(t)/dt)^2 \\
+ \sum_{t'<t} W * exp(-1/2*\sum_{i} (s_i(t')-s_i(t))^2/(\delta{}s_i)^2) \\
+ \sum_{w} (\sum_{i}c_{w,i}s_i(t) - D_w)^M/(\Sigma_w)^M
normal:
H = H_{0} + \sum_{t'<t} W * exp(-1/2*\sum_{i} (S_i(x(t'))-S_i(x(t)))^2/(\delta{}S_i)^2) \\
+ \sum_{w} (\sum_{i}c_{w,i}S_i(t) - D_w)^M/(\Sigma_w)^M
output:
H = H_{0} (only output S(x), no forces)
Here:
S(x(t)) = x
s(t) = xr
DS = Ds = delta
*/
/// Value of the colvar
colvarvalue x;
// TODO: implement functionality to treat these
// /// Vector of individual values from CVCs
// colvarvalue x_cvc;
// /// Jacobian matrix of individual values from CVCs
// colvarvalue dx_cvc;
/// Cached reported value (x may be manipulated)
colvarvalue x_reported;
/// Finite-difference velocity
colvarvalue v_fdiff;
inline colvarvalue fdiff_velocity(colvarvalue const &xold,
colvarvalue const &xnew)
{
// using the gradient of the square distance to calculate the
// velocity (non-scalar variables automatically taken into
// account)
cvm::real dt = cvm::dt();
return ( ( (dt > 0.0) ? (1.0/dt) : 1.0 ) *
0.5 * dist2_lgrad(xnew, xold) );
}
/// Cached reported velocity
colvarvalue v_reported;
// Options for extended_lagrangian
/// Restraint center
colvarvalue xr;
/// Velocity of the restraint center
colvarvalue vr;
/// Mass of the restraint center
cvm::real ext_mass;
/// Restraint force constant
cvm::real ext_force_k;
/// Friction coefficient for Langevin extended dynamics
cvm::real ext_gamma;
/// Amplitude of Gaussian white noise for Langevin extended dynamics
cvm::real ext_sigma;
/// \brief Harmonic restraint force
colvarvalue fr;
/// \brief Jacobian force, when Jacobian_force is enabled
colvarvalue fj;
/// Cached reported system force
colvarvalue ft_reported;
public:
/// \brief Bias force; reset_bias_force() should be called before
/// the biases are updated
colvarvalue fb;
/// \brief Total \em applied force; fr (if extended_lagrangian
/// is defined), fb (if biases are applied) and the walls' forces
/// (if defined) contribute to it
colvarvalue f;
/// \brief Total force, as derived from the atomic trajectory;
/// should equal the total system force plus \link f \endlink
colvarvalue ft;
/// Period, if it is a constant
cvm::real period;
/// \brief Same as above, but also takes into account components
/// with a variable period, such as distanceZ
bool b_periodic;
/// \brief Expand the boundaries of multiples of width, to keep the
/// value always within range
bool expand_boundaries;
/// \brief Location of the lower boundary
colvarvalue lower_boundary;
/// \brief Location of the lower wall
colvarvalue lower_wall;
/// \brief Force constant for the lower boundary potential (|x-xb|^2)
cvm::real lower_wall_k;
/// \brief Whether this colvar has a hard lower boundary
bool hard_lower_boundary;
/// \brief Location of the upper boundary
colvarvalue upper_boundary;
/// \brief Location of the upper wall
colvarvalue upper_wall;
/// \brief Force constant for the upper boundary potential (|x-xb|^2)
cvm::real upper_wall_k;
/// \brief Whether this colvar has a hard upper boundary
bool hard_upper_boundary;
/// \brief Is the interval defined by the two boundaries periodic?
bool periodic_boundaries() const;
/// \brief Is the interval defined by the two boundaries periodic?
bool periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) const;
/// Constructor
colvar(std::string const &conf);
/// Parse the CVC configuration and allocate their data
int init_components(std::string const &conf);
private:
/// Parse the CVC configuration for all components of a certain type
template<typename def_class_name> int init_components_type(std::string const &conf,
char const *def_desc,
char const *def_config_key);
public:
/// Get ready for a run and re-initialize internal data if needed
void setup();
/// Destructor
~colvar();
/// \brief Calculate the colvar's value and related quantities
int calc();
/// \brief Calculate a subset of the colvar components (CVCs) currently active
/// (default: all active CVCs)
/// Note: both arguments refer to the sect of *active* CVCs, not all CVCs
int calc_cvcs(int first = 0, size_t num_cvcs = 0);
/// Ensure that the selected range of CVCs is consistent
int check_cvc_range(int first_cvc, size_t num_cvcs);
/// \brief Calculate the values of the given subset of CVCs
int calc_cvc_values(int first, size_t num_cvcs);
/// \brief Same as \link colvar::calc_cvc_values \endlink but for gradients
int calc_cvc_gradients(int first, size_t num_cvcs);
/// \brief Same as \link colvar::calc_cvc_values \endlink but for system forces
int calc_cvc_sys_forces(int first, size_t num_cvcs);
/// \brief Same as \link colvar::calc_cvc_values \endlink but for Jacobian derivatives/forces
int calc_cvc_Jacobians(int first, size_t num_cvcs);
/// \brief Collect quantities from CVCs and update aggregated data for the colvar
int collect_cvc_data();
/// \brief Collect the values of the CVCs
int collect_cvc_values();
/// \brief Same as \link colvar::collect_cvc_values \endlink but for gradients
int collect_cvc_gradients();
/// \brief Same as \link colvar::collect_cvc_values \endlink but for system forces
int collect_cvc_sys_forces();
/// \brief Same as \link colvar::collect_cvc_values \endlink but for Jacobian derivatives/forces
int collect_cvc_Jacobians();
/// \brief Calculate the quantities associated to the colvar (but not to the CVCs)
int calc_colvar_properties();
/// Get the current biasing force
inline colvarvalue bias_force() const
{
return fb;
}
/// Set the total biasing force to zero
void reset_bias_force();
/// Add to the total force from biases
void add_bias_force(colvarvalue const &force);
/// \brief Collect all forces on this colvar, integrate internal
/// equations of motion of internal degrees of freedom; see also
/// colvar::communicate_forces()
/// return colvar energy if extended Lagrandian active
cvm::real update_forces_energy();
/// \brief Communicate forces (previously calculated in
/// colvar::update()) to the external degrees of freedom
void communicate_forces();
/// \brief Enables and disables individual CVCs based on flags
int set_cvc_flags(std::vector<bool> const &flags);
/// \brief Updates the flags in the CVC objects, and their number
int update_cvc_flags();
protected:
/// \brief Number of CVC objects with an active flag
size_t n_active_cvcs;
/// Sum of square coefficients for active cvcs
cvm::real active_cvc_square_norm;
/// Time step multiplier (for coarse-time-step colvars)
/// Colvar will only be calculated at those times; biases may ignore the information and
/// always update their own forces (which is typically inexpensive) especially if
/// they rely on other colvars. In this case, the colvar will accumulate forces applied between
/// colvar updates. Alternately they may use it to calculate "impulse" biasing
/// forces at longer intervals. Impulse forces must be multiplied by the timestep factor.
int time_step_factor;
/// Biasing force collected between updates, to be applied at next update for coarse-time-step colvars
colvarvalue f_accumulated;
public:
/// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags)
inline size_t num_active_cvcs() const { return n_active_cvcs; }
/// \brief returns time_step_factor
inline int get_time_step_factor() const {return time_step_factor;}
/// \brief Use the internal metrics (as from \link cvc
/// \endlink objects) to calculate square distances and gradients
///
/// Handles correctly symmetries and periodic boundary conditions
cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Use the internal metrics (as from \link cvc
/// \endlink objects) to calculate square distances and gradients
///
/// Handles correctly symmetries and periodic boundary conditions
colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Use the internal metrics (as from \link cvc
/// \endlink objects) to calculate square distances and gradients
///
/// Handles correctly symmetries and periodic boundary conditions
colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Use the internal metrics (as from \link cvc
/// \endlink objects) to wrap a value into a standard interval
///
/// Handles correctly symmetries and periodic boundary conditions
void wrap(colvarvalue &x) const;
/// Read the analysis tasks
int parse_analysis(std::string const &conf);
/// Perform analysis tasks
void analyze();
/// Read the value from a collective variable trajectory file
std::istream & read_traj(std::istream &is);
/// Output formatted values to the trajectory file
std::ostream & write_traj(std::ostream &os);
/// Write a label to the trajectory file (comment line)
std::ostream & write_traj_label(std::ostream &os);
/// Read the collective variable from a restart file
std::istream & read_restart(std::istream &is);
/// Write the collective variable to a restart file
std::ostream & write_restart(std::ostream &os);
/// Write output files (if defined, e.g. in analysis mode)
int write_output_files();
protected:
/// Previous value (to calculate velocities during analysis)
colvarvalue x_old;
/// Time series of values and velocities used in correlation
/// functions
std::list< std::list<colvarvalue> > acf_x_history, acf_v_history;
/// Time series of values and velocities used in correlation
/// functions (pointers)x
std::list< std::list<colvarvalue> >::iterator acf_x_history_p, acf_v_history_p;
/// Time series of values and velocities used in running averages
std::list< std::list<colvarvalue> > x_history;
/// Time series of values and velocities used in correlation
/// functions (pointers)x
std::list< std::list<colvarvalue> >::iterator x_history_p;
/// \brief Collective variable with which the correlation is
/// calculated (default: itself)
std::string acf_colvar_name;
/// Length of autocorrelation function (ACF)
size_t acf_length;
/// After how many steps the ACF starts
size_t acf_offset;
/// How many timesteps separate two ACF values
size_t acf_stride;
/// Number of frames for each ACF point
size_t acf_nframes;
/// Normalize the ACF to a maximum value of 1?
bool acf_normalize;
/// ACF values
std::vector<cvm::real> acf;
/// Name of the file to write the ACF
std::string acf_outfile;
/// Type of autocorrelation function (ACF)
enum acf_type_e {
/// Unset type
acf_notset,
/// Velocity ACF, scalar product between v(0) and v(t)
acf_vel,
/// Coordinate ACF, scalar product between x(0) and x(t)
acf_coor,
/// \brief Coordinate ACF, second order Legendre polynomial
/// between x(0) and x(t) (does not work with scalar numbers)
acf_p2coor
};
/// Type of autocorrelation function (ACF)
acf_type_e acf_type;
/// \brief Velocity ACF, scalar product between v(0) and v(t)
int calc_vel_acf(std::list<colvarvalue> &v_history,
colvarvalue const &v);
/// \brief Coordinate ACF, scalar product between x(0) and x(t)
/// (does not work with scalar numbers)
void calc_coor_acf(std::list<colvarvalue> &x_history,
colvarvalue const &x);
/// \brief Coordinate ACF, second order Legendre polynomial between
/// x(0) and x(t) (does not work with scalar numbers)
void calc_p2coor_acf(std::list<colvarvalue> &x_history,
colvarvalue const &x);
/// Calculate the auto-correlation function (ACF)
int calc_acf();
/// Save the ACF to a file
void write_acf(std::ostream &os);
/// Length of running average series
size_t runave_length;
/// Timesteps to skip between two values in the running average series
size_t runave_stride;
/// Name of the file to write the running average
cvm::ofstream runave_os;
/// Current value of the running average
colvarvalue runave;
/// Current value of the square deviation from the running average
cvm::real runave_variance;
/// Calculate the running average and its standard deviation
void calc_runave();
/// If extended Lagrangian active: colvar energies (kinetic and harmonic potential)
cvm::real kinetic_energy;
cvm::real potential_energy;
public:
// collective variable component base class
class cvc;
// currently available collective variable components
// scalar colvar components
class distance;
class distance_z;
class distance_xy;
class distance_inv;
class distance_pairs;
class angle;
class dipole_angle;
class dihedral;
class coordnum;
class selfcoordnum;
class h_bond;
class rmsd;
class orientation_angle;
class orientation_proj;
class tilt;
class spin_angle;
class gyration;
class inertia;
class inertia_z;
class eigenvector;
class alpha_dihedrals;
class alpha_angles;
class dihedPC;
// non-scalar components
class distance_vec;
class distance_dir;
class cartesian;
class orientation;
protected:
/// \brief Array of \link cvc \endlink objects
std::vector<cvc *> cvcs;
/// \brief Flags to enable or disable cvcs at next colvar evaluation
std::vector<bool> cvc_flags;
/// \brief Initialize the sorted list of atom IDs for atoms involved
/// in all cvcs (called when enabling f_cv_collect_gradients)
void build_atom_list(void);
private:
/// Name of scripted function to be used
std::string scripted_function;
/// Current cvc values in the order requested by script
/// when using scriptedFunction
std::vector<const colvarvalue *> sorted_cvc_values;
public:
/// \brief Sorted array of (zero-based) IDs for all atoms involved
std::vector<int> atom_ids;
/// \brief Array of atomic gradients collected from all cvcs
/// with appropriate components, rotations etc.
/// For scalar variables only!
std::vector<cvm::rvector> atomic_gradients;
inline size_t n_components() const {
return cvcs.size();
}
};
inline colvarvalue const & colvar::value() const
{
return x_reported;
}
inline colvarvalue const & colvar::actual_value() const
{
return x;
}
inline colvarvalue const & colvar::velocity() const
{
return v_reported;
}
inline colvarvalue const & colvar::system_force() const
{
return ft_reported;
}
inline void colvar::add_bias_force(colvarvalue const &force)
{
if (cvm::debug()) {
cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
}
fb += force;
}
inline void colvar::reset_bias_force() {
fb.type(value());
fb.reset();
}
#endif
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