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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8433 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-29 17:52:31 +00:00
parent 6795f0f3af
commit fee52f2fac
13 changed files with 412 additions and 134 deletions
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74
lib/colvars/colvarcomp.h
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@ -473,18 +473,18 @@ public:
};
/// \brief Colvar component: projection of the distance vector along
/// a fixed axis (colvarvalue::type_scalar type, range (-*:*))
class colvar::min_distance
/// \brief Colvar component: average distance between two groups of atoms, weighted as the sixth power,
/// as in NMR refinements (colvarvalue::type_scalar type, range (0:*))
class colvar::distance6
: public colvar::distance
{
protected:
/// Components of the distance vector orthogonal to the axis
cvm::real smoothing;
public:
min_distance (std::string const &conf);
min_distance();
virtual inline ~min_distance() {}
distance6 (std::string const &conf);
distance6();
virtual inline ~distance6() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force (colvarvalue const &force);
@ -500,7 +500,6 @@ public:
/// \brief Colvar component: Radius of gyration of an atom group
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::gyration
@ -530,6 +529,60 @@ public:
};
/// \brief Colvar component: moment of inertia of an atom group
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::inertia
: public colvar::cvc
{
protected:
/// Atoms involved
cvm::atom_group atoms;
public:
/// Constructor
inertia (std::string const &conf);
inertia();
virtual inline ~inertia() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force (colvarvalue const &force);
virtual cvm::real dist2 (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: moment of inertia of an atom group
/// around a user-defined axis (colvarvalue::type_scalar type, range [0:*))
class colvar::inertia_z
: public colvar::inertia
{
protected:
/// Vector on which the inertia tensor is projected
cvm::rvector axis;
public:
/// Constructor
inertia_z (std::string const &conf);
inertia_z();
virtual inline ~inertia_z() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force (colvarvalue const &force);
virtual cvm::real dist2 (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
};
/// \brief Colvar component: projection of 3N coordinates onto an
/// eigenvector (colvarvalue::type_scalar type, range (-*:*))
class colvar::eigenvector
@ -1223,8 +1276,7 @@ inline void colvar::spin_angle::wrap (colvarvalue &x) const
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
const cvm::real tmp = x1.real_value - x2.real_value; \
return tmp*tmp; \
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
@ -1249,12 +1301,14 @@ inline void colvar::spin_angle::wrap (colvarvalue &x) const
simple_scalar_dist_functions (distance)
// NOTE: distance_z has explicit functions, see below
simple_scalar_dist_functions (distance_xy)
simple_scalar_dist_functions (min_distance)
simple_scalar_dist_functions (distance6)
simple_scalar_dist_functions (angle)
simple_scalar_dist_functions (coordnum)
simple_scalar_dist_functions (selfcoordnum)
simple_scalar_dist_functions (h_bond)
simple_scalar_dist_functions (gyration)
simple_scalar_dist_functions (inertia)
simple_scalar_dist_functions (inertia_z)
simple_scalar_dist_functions (rmsd)
simple_scalar_dist_functions (logmsd)
simple_scalar_dist_functions (orientation_angle)