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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12650 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-10-28 19:53:17 +00:00
parent 7cea65198f
commit 51a148df16
18 changed files with 632 additions and 274 deletions
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116
lib/colvars/colvarcomp.h
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@ -219,14 +219,6 @@ public:
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Return a positive number if x2>x1, zero if x2==x1,
/// negative otherwise (can be redefined to transparently implement
/// constraints, symmetries and periodicities) \b Note: \b it \b
/// only \b works \b with \b scalar \b variables, otherwise raises
/// an error
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
/// \brief Wrapp value (for periodic/symmetric cvcs)
virtual void wrap (colvarvalue &x) const;
@ -300,18 +292,6 @@ inline colvarvalue colvar::cvc::dist2_rgrad (colvarvalue const &x1,
return x2.dist2_grad (x1);
}
inline cvm::real colvar::cvc::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
if (this->type() == colvarvalue::type_scalar) {
return cvm::real (x1 - x2);
} else {
cvm::error ("Error: you requested an operation which requires "
"comparison between two non-scalar values.\n");
return 0.0;
}
}
inline void colvar::cvc::wrap (colvarvalue &x) const
{
return;
@ -356,8 +336,6 @@ public:
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;
};
@ -383,9 +361,6 @@ public:
/// Redefined to handle the box periodicity
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the box periodicity
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
};
@ -408,8 +383,6 @@ public:
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;
};
@ -453,8 +426,6 @@ public:
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 Redefined to make use of the user-provided period
virtual void wrap (colvarvalue &x) const;
};
@ -485,8 +456,6 @@ public:
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;
};
@ -511,8 +480,6 @@ public:
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;
};
@ -541,8 +508,6 @@ public:
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;
};
@ -565,8 +530,6 @@ public:
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;
};
@ -592,8 +555,6 @@ public:
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;
};
@ -635,8 +596,6 @@ public:
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;
};
@ -685,8 +644,6 @@ public:
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;
};
@ -736,9 +693,6 @@ public:
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual void wrap (colvarvalue &x) const;
};
@ -796,8 +750,6 @@ public:
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: self-coordination number within a group
@ -835,8 +787,6 @@ public:
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: hydrogen bond, defined as the product of
@ -872,8 +822,6 @@ public:
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;
};
@ -915,8 +863,6 @@ public:
// 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;
// };
@ -958,8 +904,6 @@ public:
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: dihedPC
@ -988,8 +932,6 @@ public:
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: orientation in space of an atom group,
@ -1030,8 +972,6 @@ public:
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;
};
@ -1055,8 +995,6 @@ public:
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;
};
@ -1080,8 +1018,6 @@ public:
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;
};
@ -1108,8 +1044,6 @@ public:
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;
};
@ -1141,9 +1075,6 @@ public:
virtual colvarvalue dist2_rgrad (colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual cvm::real compare (colvarvalue const &x1,
colvarvalue const &x2) const;
/// Redefined to handle the 2*PI periodicity
virtual void wrap (colvarvalue &x) const;
};
@ -1180,8 +1111,6 @@ public:
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;
};
@ -1214,12 +1143,6 @@ public:
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
@ -1268,12 +1191,6 @@ inline colvarvalue colvar::dihedral::dist2_rgrad (colvarvalue const &x1,
return (-2.0) * diff;
}
inline cvm::real colvar::dihedral::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
return dist2_lgrad (x1, x2);
}
inline void colvar::dihedral::wrap (colvarvalue &x) const
{
if ((x.real_value - wrap_center) >= 180.0) {
@ -1313,12 +1230,6 @@ inline colvarvalue colvar::spin_angle::dist2_rgrad (colvarvalue const &x1,
return (-2.0) * diff;
}
inline cvm::real colvar::spin_angle::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
return dist2_lgrad (x1, x2);
}
inline void colvar::spin_angle::wrap (colvarvalue &x) const
{
if ((x.real_value - wrap_center) >= 180.0) {
@ -1370,12 +1281,6 @@ inline colvarvalue colvar::distance_z::dist2_rgrad (colvarvalue const &x1,
return (-2.0) * diff;
}
inline cvm::real colvar::distance_z::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
return dist2_lgrad (x1, x2);
}
inline void colvar::distance_z::wrap (colvarvalue &x) const
{
if (! this->b_periodic) {
@ -1412,13 +1317,6 @@ inline colvarvalue colvar::distance_vec::dist2_rgrad (colvarvalue const &x1,
return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
}
inline cvm::real colvar::distance_vec::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::error ("Error: cannot compare() two distance vectors.\n");
return 0.0;
}
inline cvm::real colvar::distance_dir::dist2 (colvarvalue const &x1,
colvarvalue const &x2) const
{
@ -1437,13 +1335,6 @@ inline colvarvalue colvar::distance_dir::dist2_rgrad (colvarvalue const &x1,
return colvarvalue ((x2.rvector_value - x1.rvector_value), colvarvalue::type_unitvector);
}
inline cvm::real colvar::distance_dir::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::error ("Error: cannot compare() two distance directions.\n");
return 0.0;
}
// distance between quaternions
inline cvm::real colvar::orientation::dist2 (colvarvalue const &x1,
@ -1464,12 +1355,5 @@ inline colvarvalue colvar::orientation::dist2_rgrad (colvarvalue const &x1,
return x2.quaternion_value.dist2_grad (x1);
}
inline cvm::real colvar::orientation::compare (colvarvalue const &x1,
colvarvalue const &x2) const
{
cvm::error ("Error: cannot compare() two quaternions.\n");
return 0.0;
}
#endif