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rLAMMPS lammps
colvaratoms.h
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// -*- 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
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