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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12811 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-12-02 02:09:53 +00:00
parent 9c0f849594
commit c4af1cdbbd
34 changed files with 5927 additions and 4786 deletions
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80
lib/colvars/colvarbias_meta.h
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@ -28,7 +28,7 @@ public:
Communication comm;
/// Constructor
colvarbias_meta (std::string const &conf, char const *key);
colvarbias_meta(std::string const &conf, char const *key);
/// Default constructor
colvarbias_meta();
@ -38,9 +38,9 @@ public:
virtual cvm::real update();
virtual std::istream & read_restart (std::istream &is);
virtual std::istream & read_restart(std::istream &is);
virtual std::ostream & write_restart (std::ostream &os);
virtual std::ostream & write_restart(std::ostream &os);
virtual void write_pmf();
@ -79,11 +79,11 @@ protected:
hill_iter new_hills_off_grid_begin;
/// Regenerate the hills_off_grid list
void recount_hills_off_grid (hill_iter h_first, hill_iter h_last,
void recount_hills_off_grid(hill_iter h_first, hill_iter h_last,
colvar_grid_scalar *ge);
/// Read a hill from a file
std::istream & read_hill (std::istream &is);
std::istream & read_hill(std::istream &is);
/// \brief step present in a state file
///
@ -95,15 +95,15 @@ protected:
/// \brief Add a new hill; if a .hills trajectory is written,
/// write it there; if there is more than one replica, communicate
/// it to the others
virtual std::list<hill>::const_iterator create_hill (hill const &h);
virtual std::list<hill>::const_iterator create_hill(hill const &h);
/// \brief Remove a previously saved hill (returns an iterator for
/// the next hill in the list)
virtual std::list<hill>::const_iterator delete_hill (hill_iter &h);
virtual std::list<hill>::const_iterator delete_hill(hill_iter &h);
/// \brief Calculate the values of the hills, incrementing
/// bias_energy
virtual void calc_hills (hill_iter h_first,
virtual void calc_hills(hill_iter h_first,
hill_iter h_last,
cvm::real &energy,
std::vector<colvarvalue> const &values = std::vector<colvarvalue> (0));
@ -111,7 +111,7 @@ protected:
/// \brief Calculate the forces acting on the i-th colvar,
/// incrementing colvar_forces[i]; must be called after calc_hills
/// each time the values of the colvars are changed
virtual void calc_hills_force (size_t const &i,
virtual void calc_hills_force(size_t const &i,
hill_iter h_first,
hill_iter h_last,
std::vector<colvarvalue> &forces,
@ -167,7 +167,7 @@ protected:
colvar_grid_gradient *hills_energy_gradients;
/// \brief Project the selected hills onto grids
void project_hills (hill_iter h_first, hill_iter h_last,
void project_hills(hill_iter h_first, hill_iter h_last,
colvar_grid_scalar *ge, colvar_grid_gradient *gf,
bool print_progress = false);
@ -268,28 +268,28 @@ public:
/// cv Pointer to the array of collective variables involved \param
/// replica (optional) Identity of the replica which creates the
/// hill
inline hill (cvm::real const &W_in,
inline hill(cvm::real const &W_in,
std::vector<colvar *> &cv,
cvm::real const &hill_width,
std::string const &replica_in = "")
: sW (1.0),
W (W_in),
centers (cv.size()),
widths (cv.size()),
it (cvm::it),
replica (replica_in)
: sW(1.0),
W(W_in),
centers(cv.size()),
widths(cv.size()),
it(cvm::it),
replica(replica_in)
{
for (size_t i = 0; i < cv.size(); i++) {
centers[i].type (cv[i]->type());
centers[i].type(cv[i]->value());
centers[i] = cv[i]->value();
widths[i] = cv[i]->width * hill_width;
}
if (cvm::debug())
cvm::log ("New hill, applied to "+cvm::to_str (cv.size())+
cvm::log("New hill, applied to "+cvm::to_str(cv.size())+
" collective variables, with centers "+
cvm::to_str (centers)+", widths "+
cvm::to_str (widths)+" and weight "+
cvm::to_str (W)+".\n");
cvm::to_str(centers)+", widths "+
cvm::to_str(widths)+" and weight "+
cvm::to_str(W)+".\n");
}
/// \brief General constructor: all data are explicitly passed as
@ -298,27 +298,27 @@ public:
/// weight Weight of the hill \param centers Center of the hill
/// \param widths Width of the hill around centers \param replica
/// (optional) Identity of the replica which creates the hill
inline hill (size_t const &it_in,
inline hill(size_t const &it_in,
cvm::real const &W_in,
std::vector<colvarvalue> const &centers_in,
std::vector<cvm::real> const &widths_in,
std::string const &replica_in = "")
: sW (1.0),
W (W_in),
centers (centers_in),
widths (widths_in),
it (it_in),
replica (replica_in)
: sW(1.0),
W(W_in),
centers(centers_in),
widths(widths_in),
it(it_in),
replica(replica_in)
{}
/// Copy constructor
inline hill (colvarbias_meta::hill const &h)
: sW (1.0),
W (h.W),
centers (h.centers),
widths (h.widths),
it (h.it),
replica (h.replica)
inline hill(colvarbias_meta::hill const &h)
: sW(1.0),
W(h.W),
centers(h.centers),
widths(h.widths),
it(h.it),
replica(h.replica)
{}
/// Destructor
@ -332,7 +332,7 @@ public:
}
/// Get the energy using another hill weight
inline cvm::real energy (cvm::real const &new_weight)
inline cvm::real energy(cvm::real const &new_weight)
{
return new_weight * sW * hill_value;
}
@ -344,7 +344,7 @@ public:
}
/// Set the hill value as specified
inline void value (cvm::real const &new_value)
inline void value(cvm::real const &new_value)
{
hill_value = new_value;
}
@ -356,7 +356,7 @@ public:
}
/// Scale the weight with this factor (by default 1.0 is used)
inline void scale (cvm::real const &new_scale_fac)
inline void scale(cvm::real const &new_scale_fac)
{
sW = new_scale_fac;
}
@ -368,7 +368,7 @@ public:
}
/// Get the i-th component of the center
inline colvarvalue & center (size_t const &i)
inline colvarvalue & center(size_t const &i)
{
return centers[i];
}