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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-06-27 22:48:27 +00:00
parent 38112d0063
commit 4da20dce99
30 changed files with 883 additions and 571 deletions
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153
lib/colvars/colvarcomp.h
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@ -1,6 +1,16 @@
#ifndef COLVARCOMP_H
#define COLVARCOMP_H
// Declaration of colvar::cvc base class and derived ones.
//
// Future cvc's could be declared on additional header files.
// After the declaration of a new derived class, its metric
// functions must be reimplemented as well.
// If the new cvc has no symmetry or periodicity,
// this can be done straightforwardly by using the macro:
// simple_scalar_dist_functions (derived_class)
#include <fstream>
#include <cmath>
@ -40,7 +50,7 @@
/// 2. add a call to the parser in colvar.C, within the function colvar::colvar() \par
/// 3. declare the class in colvarcomp.h \par
/// 4. implement the class in one of the files colvarcomp_*.C
///
///
/// </b>
/// The cvm::atom and cvm::atom_group classes are available to
/// transparently communicate with the simulation program. However,
@ -58,7 +68,7 @@ public:
std::string name;
/// \brief Description of the type of collective variable
///
///
/// Normally this string is set by the parent \link colvar \endlink
/// object within its constructor, when all \link cvc \endlink
/// objects are initialized; therefore the main "config string"
@ -94,7 +104,7 @@ public:
/// \brief Within the constructor, make a group parse its own
/// options from the provided configuration string
void parse_group (std::string const &conf,
void parse_group (std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional = false);
@ -164,7 +174,7 @@ public:
/// \brief 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
@ -182,7 +192,7 @@ public:
/// 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
/// \link colvarvalue \endlink member functions and access directly
@ -591,7 +601,7 @@ protected:
std::vector<cvm::atom_pos> ref_pos;
/// Geometric center of the reference coordinates
cvm::rvector ref_pos_center;
cvm::atom_pos ref_pos_center;
/// Eigenvector (of a normal or essential mode): will always have zero center
std::vector<cvm::rvector> eigenvec;
@ -691,7 +701,7 @@ protected:
/// \brief Compute system force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
public:
/// Initialize by parsing the configuration
@ -759,7 +769,7 @@ public:
static cvm::real switching_function (cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |(A1-A2)*(r0_vec)^-|1 \param r0_vec
@ -808,7 +818,7 @@ public:
static cvm::real switching_function (cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
virtual cvm::real dist2 (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
@ -822,7 +832,7 @@ public:
/// \brief Colvar component: hydrogen bond, defined as the product of
/// a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol))
/// (colvarvalue::type_scalar type, range [0:1])
class colvar::h_bond
class colvar::h_bond
: public colvar::cvc
{
protected:
@ -887,7 +897,7 @@ public:
// alpha_dihedrals();
// virtual inline ~alpha_dihedrals() {}
// virtual void calc_value();
// virtual void calc_gradients();
// virtual void calc_gradients();
// virtual void apply_force (colvarvalue const &force);
// virtual cvm::real dist2 (colvarvalue const &x1,
// colvarvalue const &x2) const;
@ -921,7 +931,7 @@ protected:
/// List of hydrogen bonds
std::vector<h_bond *> hb;
/// Contribution of the hb terms
/// Contribution of the hb terms
cvm::real hb_coeff;
public:
@ -1140,6 +1150,62 @@ public:
};
// metrics functions for cvc implementations
// simple definitions of the distance functions; these are useful only
// for optimization (the type check performed in the default
// colvarcomp functions is skipped)
// definitions assuming the scalar type
#define simple_scalar_dist_functions(TYPE) \
\
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return 2.0 * (x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x2, x1); \
} \
\
inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x1, x2); \
} \
\
simple_scalar_dist_functions (distance)
// NOTE: distance_z has explicit functions, see below
simple_scalar_dist_functions (distance_xy)
simple_scalar_dist_functions (distance_inv)
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 (orientation_angle)
simple_scalar_dist_functions (tilt)
simple_scalar_dist_functions (eigenvector)
// simple_scalar_dist_functions (alpha_dihedrals)
simple_scalar_dist_functions (alpha_angles)
simple_scalar_dist_functions (dihedPC)
// metrics functions for cvc implementations with a periodicity
inline cvm::real colvar::dihedral::dist2 (colvarvalue const &x1,
@ -1177,12 +1243,12 @@ inline void colvar::dihedral::wrap (colvarvalue &x) const
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
}
return;
}
@ -1222,68 +1288,16 @@ inline void colvar::spin_angle::wrap (colvarvalue &x) const
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
}
return;
}
// simple definitions of the distance functions; these are useful only
// for optimization (the type check performed in the default
// colvarcomp functions is skipped)
// definitions assuming the scalar type
#define simple_scalar_dist_functions(TYPE) \
\
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return 2.0 * (x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x2, x1); \
} \
\
inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x1, x2); \
} \
\
simple_scalar_dist_functions (distance)
// NOTE: distance_z has explicit functions, see below
simple_scalar_dist_functions (distance_xy)
simple_scalar_dist_functions (distance_inv)
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 (orientation_angle)
simple_scalar_dist_functions (tilt)
simple_scalar_dist_functions (eigenvector)
// simple_scalar_dist_functions (alpha_dihedrals)
simple_scalar_dist_functions (alpha_angles)
simple_scalar_dist_functions (dihedPC)
// Projected distance
// Differences should always be wrapped around 0 (ignoring wrap_center)
@ -1422,9 +1436,6 @@ inline cvm::real colvar::orientation::compare (colvarvalue const &x1,
}
#endif