Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F79822119
colvaratoms.h
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Aug 28, 10:27
Size
11 KB
Mime Type
text/x-c++
Expires
Fri, Aug 30, 10:27 (2 d)
Engine
blob
Format
Raw Data
Handle
20194220
Attached To
rLAMMPS lammps
colvaratoms.h
View Options
#ifndef COLVARATOMS_H
#define COLVARATOMS_H
#include "colvarmodule.h"
#include "colvarparse.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 (although not necessarily) to keep atomic
/// data (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.
///
/// Read/write operations depend on the underlying code: hence, some
/// member functions are defined in colvarproxy_xxx.h.
class colvarmodule::atom {
protected:
/// \brief Index in the list of atoms involved by the colvars (\b
/// NOT in the global topology!)
size_t index;
public:
/// Internal identifier (zero-based)
int id;
/// Mass
cvm::real mass;
/// \brief Current position (copied from the program, can be
/// manipulated)
cvm::atom_pos pos;
/// \brief Current velocity (copied from the program, can be
/// manipulated)
cvm::rvector vel;
/// \brief System force at the previous step (copied from the
/// program, can be manipulated)
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, setting id to a non-valid value
inline 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 const &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 = std::string (""));
/// Copy constructor
atom (atom const &a);
/// Destructor
~atom();
/// Set non-constant data (everything except id and mass) to zero
inline void reset_data() {
pos = atom_pos (0.0);
vel = grad = system_force = rvector (0.0);
}
/// Get the current position
void read_position();
/// Get the current velocity
void read_velocity();
/// Get the system force
void read_system_force();
/// \brief Apply a force to the atom
///
/// The force will be used later by the MD integrator, the
/// collective variables 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 add to the existing MD force.
void apply_force (cvm::rvector const &new_force);
};
/// \brief Group of \link atom \endlink objects, mostly used by a
/// \link cvc \endlink
///
/// This class inherits from \link colvarparse \endlink and from
/// std::vector<colvarmodule::atom>, and hence all functions and
/// operators (including the bracket operator, group[i]) can be used
/// on an \link atom_group \endlink object. It can be initialized as
/// a vector, or by parsing a keyword in the configuration.
class colvarmodule::atom_group
: public std::vector<cvm::atom>,
public colvarparse
{
public:
// Note: all members here are kept public, to make possible to any
// object accessing and manipulating them
/// \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;
/// \brief dummy atom position
cvm::atom_pos dummy_atom_pos;
/// 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
void create_sorted_ids (void);
/// \brief Before calculating colvars, move the group to overlap the
/// center of mass of reference coordinates
bool b_center;
/// \brief Right after updating atom coordinates (and after
/// centering coordinates, if b_center is true), rotate the group to
/// overlap the reference coordinates. You should not manipulate
/// atoms individually if you turn on this flag.
///
/// 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;
/// Rotation between the group and its reference coordinates
cvm::rotation rot;
/// \brief In case b_center or b_rotate is true, use these reference
/// coordinates
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 In case b_center or b_rotate is true, fit this group to
/// the reference positions (default: the parent group itself)
atom_group *ref_pos_group;
/// Total mass of the atom group
cvm::real total_mass;
/// \brief Don't apply any force on this group (use its coordinates
/// only to calculate a colvar)
bool noforce;
/// \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,
atom_group *ref_pos_group = NULL);
/// \brief Initialize the group by looking up its configuration
/// string in conf and parsing it
void parse (std::string const &conf,
char const *key,
atom_group *ref_pos_group = NULL);
/// \brief Initialize the group after a temporary vector of atoms
atom_group (std::vector<cvm::atom> const &atoms);
/// \brief Add an atom to this group
void add_atom (cvm::atom const &a);
/// \brief Default constructor
atom_group();
/// \brief Destructor
~atom_group();
/// \brief Get the current positions; if b_center or b_rotate are
/// true, center and/or rotate the coordinates right after reading
/// them
void read_positions();
/// \brief Move all positions
void apply_translation (cvm::rvector const &t);
/// \brief Rotate all positions
void apply_rotation (cvm::rotation const &q);
/// \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 = this->begin(); ai != this->end(); ai++)
ai->reset_data();
}
/// \brief Return a copy of the current atom positions
std::vector<cvm::atom_pos> positions() const;
/// \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 the center of geometry of the positions \param ref_pos
/// Use the closest periodic images to this position
cvm::atom_pos center_of_geometry (cvm::atom_pos const &ref_pos);
/// \brief Return the center of geometry of the positions, assuming
/// that coordinates are already pbc-wrapped
cvm::atom_pos center_of_geometry() const;
/// \brief Return the center of mass of the positions \param ref_pos
/// Use the closest periodic images to this position
cvm::atom_pos center_of_mass (cvm::atom_pos const &ref_pos);
/// \brief Return the center of mass of the positions, assuming that
/// coordinates are already pbc-wrapped
cvm::atom_pos center_of_mass() const;
/// \brief Store atom positions from the previous step
std::vector<cvm::atom_pos> old_pos;
/// \brief Return a copy of the current atom velocities
std::vector<cvm::rvector> velocities() const;
/// \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 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 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);
/// \brief Apply an array of forces directly on the individual
/// atoms; the length of the specified vector must be the same of
/// this \link atom_group \endlink.
///
/// If the group is being rotated to a reference frame (e.g. to
/// express the colvar independently from the solute rotation), the
/// forces are 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 forces.
void apply_forces (std::vector<cvm::rvector> const &forces);
};
#endif
// Emacs
// Local Variables:
// mode: C++
// End:
Event Timeline
Log In to Comment