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colvar::min_distance Class Reference

Colvar component: projection of the distance vector along a fixed axis (colvarvalue::type_scalar type, range (-*:*)). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::min_distance:

colvar::distance colvar::cvc colvarparse List of all members.

Public Member Functions

 min_distance (std::string const &conf)
 min_distance ()
virtual ~min_distance ()
virtual void calc_value ()
 Calculate the variable.
virtual void calc_gradients ()
 Calculate the atomic gradients, to be reused later in order to apply forces.
virtual void apply_force (colvarvalue const &force)
 Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function).
virtual cvm::real dist2 (colvarvalue const &x1, colvarvalue const &x2) const
 Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
 Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
 Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual cvm::real compare (colvarvalue const &x1, colvarvalue const &x2) const
 Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error.

Protected Attributes

cvm::real smoothing
 Components of the distance vector orthogonal to the axis.

Detailed Description

Colvar component: projection of the distance vector along a fixed axis (colvarvalue::type_scalar type, range (-*:*)).

Definition at line 458 of file colvarcomp.h.

Constructor & Destructor Documentation

colvar::min_distance::min_distance (  std::string const &  conf  ) 
 

Definition at line 335 of file colvarcomp_distances.C.

References smoothing, and colvarvalue::type().

00336   : distance (conf)
00337 {
00338   function_type = "min_distance";
00339   x.type (colvarvalue::type_scalar);
00340 
00341   get_keyval (conf, "smoothing", smoothing, (1.0 * cvm::unit_angstrom()));
00342 }

colvar::min_distance::min_distance (   ) 
 

Definition at line 344 of file colvarcomp_distances.C.

References colvarvalue::type().

00345   : distance()
00346 {
00347   function_type = "min_distance";
00348   x.type (colvarvalue::type_scalar);
00349 }

virtual colvar::min_distance::~min_distance (   )  [inline, virtual]
 

Definition at line 467 of file colvarcomp.h.

00467 {}

Member Function Documentation

void colvar::min_distance::apply_force (  colvarvalue const &  force  )  [virtual]
 

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function).

Note: multiple calls to this function within the same simulation step will add the forces altogether

Parameters:
cvforce The collective variable force, usually coming from the biases and eventually manipulated by the parent object

Reimplemented from colvar::distance.

Definition at line 401 of file colvarcomp_distances.C.

References colvarmodule::atom_group::apply_colvar_force(), colvarmodule::atom_group::noforce, and colvarvalue::real_value.

00402 {
00403   if (!group1.noforce)
00404     group1.apply_colvar_force (force.real_value);
00405 
00406   if (!group2.noforce)
00407     group2.apply_colvar_force (force.real_value);
00408 }

void colvar::min_distance::calc_gradients (   )  [virtual]
 

Calculate the atomic gradients, to be reused later in order to apply forces.

Reimplemented from colvar::distance.

Definition at line 377 of file colvarcomp_distances.C.

References colvarmodule::rvector::norm(), colvarmodule::position_distance(), colvarvalue::real_value, and smoothing.

00378 {
00379   if (x.real_value > 0.0) {
00380     cvm::real const sum = ::exp (smoothing/x.real_value);
00381     cvm::real const dxdsum = -1.0 *
00382       (x.real_value/smoothing) * (x.real_value/smoothing) *
00383       (1.0 / sum);
00384 
00385     for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
00386       for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
00387         cvm::rvector const dv = cvm::position_distance (ai1->pos, ai2->pos);
00388         cvm::real const d = dv.norm();
00389         if (d > 0.0) {
00390           cvm::rvector const dvu = dv / dv.norm();
00391           ai1->grad += dxdsum * ::exp (smoothing / d) *
00392             smoothing * (-1.0/(d*d)) * (-1.0) * dvu;
00393           ai2->grad += dxdsum * ::exp (smoothing / d) *
00394             smoothing * (-1.0/(d*d)) * dvu;
00395         }
00396       }
00397     }
00398   }
00399 }

void colvar::min_distance::calc_value (   )  [virtual]
 

Calculate the variable.

Reimplemented from colvar::distance.

Definition at line 351 of file colvarcomp_distances.C.

References colvarmodule::rvector::norm(), colvarmodule::position_distance(), colvarmodule::atom_group::read_positions(), colvarvalue::real_value, colvarmodule::atom_group::reset_atoms_data(), and smoothing.

00352 {
00353   group1.reset_atoms_data();
00354   group2.reset_atoms_data();
00355 
00356   group1.read_positions();
00357   group2.read_positions();
00358 
00359   x.real_value = 0.0;
00360 
00361   bool zero_dist = false;
00362 
00363   for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
00364     for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
00365       cvm::rvector const dv = cvm::position_distance (ai1->pos, ai2->pos);
00366       cvm::real const d = dv.norm();
00367       if (d > 0.0)
00368         x.real_value += ::exp (smoothing / d);
00369       else
00370         zero_dist = true;
00371     }
00372   }
00373 
00374   x.real_value = zero_dist ? 0.0 : smoothing/(::log (x.real_value));
00375 }

virtual cvm::real colvar::min_distance::compare (  colvarvalue const &  x1,
colvarvalue const &  x2
)  const [virtual]
 

Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error.

Reimplemented from colvar::distance.

virtual cvm::real colvar::min_distance::dist2 (  colvarvalue const &  x1,
colvarvalue const &  x2
)  const [virtual]
 

Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities).

colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object.

If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients.

If constraints are present (and not already implemented by any of the types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface.

Finally, another useful application, if you are performing very many operations with these functions, could be to override the member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar type.

Reimplemented from colvar::distance.

virtual colvarvalue colvar::min_distance::dist2_lgrad (  colvarvalue const &  x1,
colvarvalue const &  x2
)  const [virtual]
 

Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::distance.

virtual colvarvalue colvar::min_distance::dist2_rgrad (  colvarvalue const &  x1,
colvarvalue const &  x2
)  const [virtual]
 

Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::distance.

Member Data Documentation

cvm::real colvar::min_distance::smoothing [protected]
 

Components of the distance vector orthogonal to the axis.

Definition at line 463 of file colvarcomp.h.

Referenced by calc_gradients(), calc_value(), and min_distance().

The documentation for this class was generated from the following files:
Generated on Mon Nov 23 04:59:32 2009 for NAMD by  doxygen 1.3.9.1