Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/lib/colvars/colvaratoms.h
48cec4d7d21aefficient_neuronet

Last Change
Raw File

colvaratoms.h
View Options

// -*- c++ -*-
#ifndef COLVARATOMS_H
#define COLVARATOMS_H
#include "colvarmodule.h"
#include "colvarparse.h"
#include "colvardeps.h"
/// \brief Stores numeric id, mass and all mutable data for an atom,
/// mostly used by a \link cvc \endlink
///
/// This class may be used to keep atomic data such as id, mass,
/// position and collective variable derivatives) altogether.
/// There may be multiple instances with identical
/// numeric id, all acting independently: forces communicated through
/// these instances will be summed together.
class colvarmodule::atom {
protected:
/// Index in the colvarproxy arrays (\b NOT in the global topology!)
int index;
public:
/// Identifier for the MD program (0-based)
int id;
/// Mass
cvm::real mass;
/// Charge
cvm::real charge;
/// \brief Current position (copied from the program, can be
/// modified if necessary)
cvm::atom_pos pos;
/// \brief Current velocity (copied from the program, can be
/// modified if necessary)
cvm::rvector vel;
/// \brief System force at the previous step (copied from the
/// program, can be modified if necessary)
cvm::rvector system_force;
/// \brief Gradient of a scalar collective variable with respect
/// to this atom
///
/// This can only handle a scalar collective variable (i.e. when
/// the \link colvarvalue::real_value \endlink member is used
/// from the \link colvarvalue \endlink class), which is also the
/// most frequent case. For more complex types of \link
/// colvarvalue \endlink objects, atomic gradients should be
/// defined within the specific \link cvc \endlink
/// implementation
cvm::rvector grad;
/// \brief Default constructor (sets index and id both to -1)
atom();
/// \brief Initialize an atom for collective variable calculation
/// and get its internal identifier \param atom_number Atom index in
/// the system topology (starting from 1)
atom(int atom_number);
/// \brief Initialize an atom for collective variable calculation
/// and get its internal identifier \param residue Residue number
/// \param atom_name Name of the atom in the residue \param
/// segment_id For PSF topologies, the segment identifier; for other
/// type of topologies, may not be required
atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id);
/// Copy constructor
atom(atom const &a);
/// Destructor
~atom();
/// Set mutable data (everything except id and mass) to zero; update mass
inline void reset_data()
{
pos = cvm::atom_pos(0.0);
vel = grad = system_force = cvm::rvector(0.0);
}
/// Get the latest value of the mass
inline void update_mass()
{
mass = (cvm::proxy)->get_atom_mass(index);
}
/// Get the latest value of the charge
inline void update_charge()
{
charge = (cvm::proxy)->get_atom_charge(index);
}
/// Get the current position
inline void read_position()
{
pos = (cvm::proxy)->get_atom_position(index);
}
/// Get the current velocity
inline void read_velocity()
{
vel = (cvm::proxy)->get_atom_velocity(index);
}
/// Get the system force
inline void read_system_force()
{
system_force = (cvm::proxy)->get_atom_system_force(index);
}
/// \brief Apply a force to the atom
///
/// Note: the force is not applied instantly, but will be used later
/// by the MD integrator (the colvars module does not integrate
/// equations of motion.
///
/// Multiple calls to this function by either the same
/// \link atom \endlink object or different objects with identical
/// \link id \endlink will all be added together.
inline void apply_force(cvm::rvector const &new_force) const
{
(cvm::proxy)->apply_atom_force(index, new_force);
}
};
/// \brief Group of \link atom \endlink objects, mostly used by a
/// \link cvc \endlink object to gather all atomic data
class colvarmodule::atom_group
: public colvarparse, public cvm::deps
{
public:
/// \brief Initialize the group by looking up its configuration
/// string in conf and parsing it; this is actually done by parse(),
/// which is a member function so that a group can be initialized
/// also after construction
atom_group(std::string const &conf,
char const *key);
/// \brief Keyword used to define the group
// TODO Make this field part of the data structures that link a group to a CVC
std::string key;
/// \brief Set default values for common flags
int init();
/// \brief Update data required to calculate cvc's
int setup();
/// \brief Initialize the group by looking up its configuration
/// string in conf and parsing it
int parse(std::string const &conf);
int add_atom_numbers(std::string const &numbers_conf);
int add_index_group(std::string const &index_group_name);
int add_atom_numbers_range(std::string const &range_conf);
int add_atom_name_residue_range(std::string const &psf_segid,
std::string const &range_conf);
int parse_fitting_options(std::string const &group_conf);
/// \brief Initialize the group after a (temporary) vector of atoms
atom_group(std::vector<cvm::atom> const &atoms_in);
/// \brief Add an atom object to this group
int add_atom(cvm::atom const &a);
/// \brief Add an atom ID to this group (the actual atomicdata will be not be handled by the group)
int add_atom_id(int aid);
/// \brief Remove an atom object from this group
int remove_atom(cvm::atom_iter ai);
/// \brief Re-initialize the total mass of a group.
/// This is needed in case the hosting MD code has an option to
/// change atom masses after their initialization.
void reset_mass(std::string &name, int i, int j);
/// \brief Implementation of the feature list for atom group
static std::vector<feature *> ag_features;
/// \brief Implementation of the feature list accessor for atom group
virtual std::vector<feature *> &features() {
return ag_features;
}
/// \brief Default constructor
atom_group();
/// \brief Destructor
~atom_group();
protected:
/// \brief Array of atom objects
std::vector<cvm::atom> atoms;
/// \brief Array of atom identifiers for the MD program (0-based)
std::vector<int> atoms_ids;
/// \brief Dummy atom position
cvm::atom_pos dummy_atom_pos;
/// \brief Index in the colvarproxy arrays (if the group is scalable)
int index;
public:
inline cvm::atom & operator [] (size_t const i)
{
return atoms[i];
}
inline cvm::atom const & operator [] (size_t const i) const
{
return atoms[i];
}
inline cvm::atom_iter begin()
{
return atoms.begin();
}
inline cvm::atom_const_iter begin() const
{
return atoms.begin();
}
inline cvm::atom_iter end()
{
return atoms.end();
}
inline cvm::atom_const_iter end() const
{
return atoms.end();
}
inline size_t size() const
{
return atoms.size();
}
/// \brief If this option is on, this group merely acts as a wrapper
/// for a fixed position; any calls to atoms within or to
/// functions that return disaggregated data will fail
bool b_dummy;
/// Sorted list of zero-based (internal) atom ids
/// (populated on-demand by create_sorted_ids)
std::vector<int> sorted_ids;
/// Allocates and populates the sorted list of atom ids
int create_sorted_ids(void);
/// \brief When updating atomic coordinates, translate them to align with the
/// center of mass of the reference coordinates
bool b_center;
/// \brief When updating atom coordinates (and after
/// centering them if b_center is set), rotate the group to
/// align with the reference coordinates.
///
/// Note: gradients will be calculated in the rotated frame: when
/// forces will be applied, they will rotated back to the original
/// frame
bool b_rotate;
/// The rotation calculated automatically if b_rotate is defined
cvm::rotation rot;
/// \brief Indicates that the user has explicitly set centerReference or
/// rotateReference, and the corresponding reference:
/// cvc's (eg rmsd, eigenvector) will not override the user's choice
bool b_user_defined_fit;
/// \brief Whether or not the derivatives of the roto-translation
/// should be included when calculating the colvar's gradients (default: yes)
bool b_fit_gradients;
/// \brief use reference coordinates for b_center or b_rotate
std::vector<cvm::atom_pos> ref_pos;
/// \brief Center of geometry of the reference coordinates; regardless
/// of whether b_center is true, ref_pos is centered to zero at
/// initialization, and ref_pos_cog serves to center the positions
cvm::atom_pos ref_pos_cog;
/// \brief If b_center or b_rotate is true, use this group to
/// define the transformation (default: this group itself)
atom_group *fitting_group;
/// Total mass of the atom group
cvm::real total_mass;
void update_total_mass();
/// Total charge of the atom group
cvm::real total_charge;
void update_total_charge();
/// \brief Don't apply any force on this group (use its coordinates
/// only to calculate a colvar)
bool noforce;
/// \brief Get the current positions
void read_positions();
/// \brief (Re)calculate the optimal roto-translation
void calc_apply_roto_translation();
/// \brief Save aside the center of geometry of the reference positions,
/// then subtract it from them
///
/// In this way it will be possible to use ref_pos also for the
/// rotational fit.
/// This is called either by atom_group::parse or by CVCs that assign
/// reference positions (eg. RMSD, eigenvector).
void center_ref_pos();
/// \brief Move all positions
void apply_translation(cvm::rvector const &t);
/// \brief Get the current velocities; this must be called always
/// *after* read_positions(); if b_rotate is defined, the same
/// rotation applied to the coordinates will be used
void read_velocities();
/// \brief Get the current system_forces; this must be called always
/// *after* read_positions(); if b_rotate is defined, the same
/// rotation applied to the coordinates will be used
void read_system_forces();
/// Call reset_data() for each atom
inline void reset_atoms_data()
{
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++)
ai->reset_data();
if (fitting_group)
fitting_group->reset_atoms_data();
}
/// \brief Recompute all mutable quantities that are required to compute CVCs
int calc_required_properties();
/// \brief Return a copy of the current atom positions
std::vector<cvm::atom_pos> positions() const;
/// \brief Calculate the center of geometry of the atomic positions, assuming
/// that they are already pbc-wrapped
int calc_center_of_geometry();
private:
/// \brief Center of geometry
cvm::atom_pos cog;
/// \brief Center of geometry before any fitting
cvm::atom_pos cog_orig;
public:
/// \brief Return the center of geometry of the atomic positions
inline cvm::atom_pos center_of_geometry() const
{
return cog;
}
/// \brief Calculate the center of mass of the atomic positions, assuming that
/// they are already pbc-wrapped
int calc_center_of_mass();
private:
/// \brief Center of mass
cvm::atom_pos com;
/// \brief The derivative of a scalar variable with respect to the COM
// TODO for scalable calculations of more complex variables (e.g. rotation),
// use a colvarvalue of vectors to hold the entire derivative
cvm::rvector scalar_com_gradient;
public:
/// \brief Return the center of mass of the atomic positions
inline cvm::atom_pos center_of_mass() const
{
return com;
}
/// \brief Return a copy of the current atom positions, shifted by a constant vector
std::vector<cvm::atom_pos> positions_shifted(cvm::rvector const &shift) const;
/// \brief Return a copy of the current atom velocities
std::vector<cvm::rvector> velocities() const;
///\brief Calculate the dipole of the atom group around the specified center
int calc_dipole(cvm::atom_pos const &com);
private:
cvm::rvector dip;
public:
///\brief Return the (previously calculated) dipole of the atom group
inline cvm::rvector dipole() const
{
return dip;
}
/// \brief Return a copy of the system forces
std::vector<cvm::rvector> system_forces() const;
/// \brief Return a copy of the aggregated total force on the group
cvm::rvector system_force() const;
/// \brief Shorthand: save the specified gradient on each atom,
/// weighting with the atom mass (mostly used in combination with
/// \link center_of_mass() \endlink)
void set_weighted_gradient(cvm::rvector const &grad);
/// \brief Calculate the derivatives of the fitting transformation
void calc_fit_gradients();
/// \brief Derivatives of the fitting transformation
std::vector<cvm::atom_pos> fit_gradients;
/// \brief Used by a (scalar) colvar to apply its force on its \link
/// atom_group \endlink members
///
/// The (scalar) force is multiplied by the colvar gradient for each
/// atom; this should be used when a colvar with scalar \link
/// colvarvalue \endlink type is used (this is the most frequent
/// case: for colvars with a non-scalar type, the most convenient
/// solution is to sum together the Cartesian forces from all the
/// colvar components, and use apply_force() or apply_forces()). If
/// the group is being rotated to a reference frame (e.g. to express
/// the colvar independently from the solute rotation), the
/// gradients are temporarily rotated to the original frame.
void apply_colvar_force(cvm::real const &force);
/// \brief Apply a force "to the center of mass", i.e. the force is
/// distributed on each atom according to its mass
///
/// If the group is being rotated to a reference frame (e.g. to
/// express the colvar independently from the solute rotation), the
/// force is rotated back to the original frame. Colvar gradients
/// are not used, either because they were not defined (e.g because
/// the colvar has not a scalar value) or the biases require to
/// micromanage the force.
void apply_force(cvm::rvector const &force);
};
#endif
c4science · Help