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Update Colvars library to version 2024-06-04

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This commit is contained in:
Giacomo Fiorin
2024-08-06 01:07:43 +02:00
parent 278accd9ea
commit 133dee9ac1
74 changed files with 7343 additions and 4676 deletions
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104
lib/colvars/colvar.h
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@ -10,12 +10,11 @@
#ifndef COLVAR_H
#define COLVAR_H
#include <iostream>
#if (__cplusplus >= 201103L)
#include <map>
#include <functional>
#endif
#include <list>
#include <iosfwd>
#include <map>
#include <memory>
#include "colvarmodule.h"
#include "colvarvalue.h"
@ -91,7 +90,7 @@ public:
/// calculations, \link colvarbias_abf \endlink, it is used to
/// calculate the grid spacing in the direction of this collective
/// variable.
cvm::real width;
cvm::real width = 1.0;
/// \brief Implementation of the feature list for colvar
static std::vector<feature *> cv_features;
@ -184,13 +183,13 @@ protected:
/// Previous velocity of the restraint center
colvarvalue prev_v_ext;
/// Mass of the restraint center
cvm::real ext_mass;
cvm::real ext_mass = 0.0;
/// Restraint force constant
cvm::real ext_force_k;
cvm::real ext_force_k = 0.0;
/// Friction coefficient for Langevin extended dynamics
cvm::real ext_gamma;
cvm::real ext_gamma = 0.0;
/// Amplitude of Gaussian white noise for Langevin extended dynamics
cvm::real ext_sigma;
cvm::real ext_sigma = 0.0;
/// \brief Applied force on extended DOF, for output (unscaled if using MTS)
colvarvalue fr;
@ -224,14 +223,14 @@ public:
colvarvalue ft;
/// Period, if this variable is periodic
cvm::real period;
cvm::real period = 0.0;
/// Center of wrapping, if this variable is periodic
cvm::real wrap_center;
cvm::real wrap_center = 0.0;
/// \brief Expand the boundaries of multiples of width, to keep the
/// value always within range
bool expand_boundaries;
bool expand_boundaries = false;
/// \brief Location of the lower boundary
colvarvalue lower_boundary;
@ -252,6 +251,9 @@ public:
/// Main init function
int init(std::string const &conf);
/// Populate the map of available CVC types
void define_component_types();
/// Parse the CVC configuration and allocate their data
int init_components(std::string const &conf);
@ -271,17 +273,13 @@ public:
virtual int init_dependencies();
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);
#if (__cplusplus >= 201103L)
/// For the C++11 case, the names of all available components are
/// registered in the global map at first, and then the CVC configuration
/// is parsed by this function
int init_components_type_from_global_map(const std::string& conf,
const char* def_config_key);
#endif
/// Declare an available CVC type and its description, register them in the global map
template <typename def_class_name>
void add_component_type(char const *description, char const *config_key);
/// Initialize any CVC objects matching the given key
int init_components_type(const std::string &conf, const char *config_key);
public:
@ -387,10 +385,10 @@ public:
protected:
/// \brief Number of CVC objects with an active flag
size_t n_active_cvcs;
size_t n_active_cvcs = 0;
/// Sum of square coefficients for active cvcs
cvm::real active_cvc_square_norm;
cvm::real active_cvc_square_norm = 0.0;
/// Update the sum of square coefficients for active cvcs
void update_active_cvc_square_norm();
@ -460,16 +458,35 @@ public:
/// 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
/// Read the colvar's state from a formatted input stream
std::istream & read_state(std::istream &is);
/// Write the collective variable to a restart file
std::ostream & write_state(std::ostream &os);
/// Read the colvar's state from an unformatted input stream
cvm::memory_stream & read_state(cvm::memory_stream &is);
/// Check the name of the bias vs. the given string, set the matching_state flag accordingly
int check_matching_state(std::string const &state_conf);
/// Read the values of colvar mutable data from a string (used by both versions of read_state())
int set_state_params(std::string const &state_conf);
/// Write the state information of this colvar in a block of text, suitable for later parsing
std::string const get_state_params() const;
/// Write the colvar's state to a formatted output stream
std::ostream & write_state(std::ostream &os) const;
/// Write the colvar's state to an unformatted output stream
cvm::memory_stream & write_state(cvm::memory_stream &os) const;
/// Write output files (if defined, e.g. in analysis mode)
int write_output_files();
protected:
/// Flag used to tell if the state string being read is for this colvar
bool matching_state;
/// Previous value (to calculate velocities during analysis)
colvarvalue x_old;
@ -554,15 +571,15 @@ protected:
/// Current value of the running average
colvarvalue runave;
/// Current value of the square deviation from the running average
cvm::real runave_variance;
cvm::real runave_variance = 0.0;
/// Calculate the running average and its standard deviation
int calc_runave();
/// If extended Lagrangian active: colvar kinetic energy
cvm::real kinetic_energy;
cvm::real kinetic_energy = 0.0;
/// If extended Lagrangian active: colvar harmonic potential
cvm::real potential_energy;
cvm::real potential_energy = 0.0;
public:
@ -601,8 +618,9 @@ public:
class dihedPC;
class alch_lambda;
class alch_Flambda;
class componentDisabled;
class CartesianBasedPath;
class aspath;
class azpath;
class gspath;
class gzpath;
class linearCombination;
@ -626,21 +644,19 @@ public:
// components that do not handle any atoms directly
class map_total;
/// getter of the global cvc map
#if (__cplusplus >= 201103L)
/// A global mapping of cvc names to the cvc constructors
static const std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& get_global_cvc_map() {
return global_cvc_map;
static const std::map<std::string, std::function<colvar::cvc *()>> &get_global_cvc_map()
{
return global_cvc_map;
}
#endif
/// \brief function for sorting cvcs by their names
static bool compare_cvc(const colvar::cvc* const i, const colvar::cvc* const j);
protected:
/// \brief Array of \link colvar::cvc \endlink objects
std::vector<cvc *> cvcs;
/// Array of components objects
std::vector<std::shared_ptr<colvar::cvc>> cvcs;
/// \brief Flags to enable or disable cvcs at next colvar evaluation
std::vector<bool> cvc_flags;
@ -671,10 +687,11 @@ protected:
double dev_null;
#endif
#if (__cplusplus >= 201103L)
/// A global mapping of cvc names to the cvc constructors
static std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> global_cvc_map;
#endif
static std::map<std::string, std::function<colvar::cvc *()>> global_cvc_map;
/// A global mapping of cvc names to the corresponding descriptions
static std::map<std::string, std::string> global_cvc_desc_map;
/// Volmap numeric IDs, one for each CVC (-1 if not available)
std::vector<int> volmap_ids_;
@ -762,4 +779,3 @@ inline void colvar::reset_bias_force() {
}
#endif