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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8996 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-10-23 16:57:29 +00:00
parent c524604ec7
commit fdce177203
8 changed files with 263 additions and 310 deletions
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44
lib/colvars/colvarcomp.h
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@ -1107,11 +1107,15 @@ public:
/// colvar::orientation \endlink to calculate the rotation matrix
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::rmsd
: public colvar::orientation
: public colvar::cvc
{
protected:
/// Sum of the squares of ref_coords
cvm::real ref_pos_sum2;
/// Atom group
cvm::atom_group atoms;
/// Reference coordinates (for RMSD calculation only)
std::vector<cvm::atom_pos> ref_pos;
public:
@ -1134,39 +1138,6 @@ public:
};
/// \brief Colvar component: mean square deviation (RMSD) of a
/// group with respect to a set of reference coordinates; uses \link
/// colvar::orientation \endlink to calculate the rotation matrix
/// (colvarvalue::type_scalar type, range [0:*))
class colvar::logmsd
: public colvar::orientation
{
protected:
/// Sum of the squares of ref_coords
cvm::real ref_pos_sum2;
cvm::real MSD;
public:
/// Constructor
logmsd (std::string const &conf);
virtual inline ~logmsd() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void calc_force_invgrads();
virtual void calc_Jacobian_derivative();
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;
};
// metrics functions for cvc implementations with a periodicity
@ -1305,7 +1276,6 @@ inline void colvar::spin_angle::wrap (colvarvalue &x) const
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)
simple_scalar_dist_functions (tilt)
simple_scalar_dist_functions (eigenvector)