Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80418065
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
Sat, Aug 31, 15:15
Size
13 KB
Mime Type
text/x-c++
Expires
Mon, Sep 2, 15:15 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
20233720
Attached To
rLAMMPS lammps
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
Event Timeline
Log In to Comment