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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9395 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-02-01 22:39:47 +00:00
parent f0c4f5680b
commit df9c70770d
10 changed files with 626 additions and 373 deletions
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94
lib/colvars/colvarbias_meta.cpp
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@ -49,6 +49,15 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
get_keyval (conf, "hillWidth", hill_width, std::sqrt (2.0 * PI) / 2.0);
{
bool b_replicas = false;
get_keyval (conf, "multipleReplicas", b_replicas, false);
if (b_replicas)
comm = multiple_replicas;
else
comm = single_replica;
}
get_keyval (conf, "useGrids", use_grids, true);
if (use_grids) {
@ -84,15 +93,6 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
dump_replica_fes = false;
}
{
bool b_replicas = false;
get_keyval (conf, "multipleReplicas", b_replicas, false);
if (b_replicas)
comm = multiple_replicas;
else
comm = single_replica;
}
if (comm != single_replica) {
if (expand_grids)
@ -373,34 +373,36 @@ cvm::real colvarbias_meta::update()
int &new_size = new_sizes[i];
bool changed_lb = false, changed_ub = false;
if (curr_bin[i] < min_buffer) {
int const extra_points = (min_buffer - curr_bin[i]);
new_lb -= extra_points * colvars[i]->width;
new_size += extra_points;
// changed offset in this direction => the pointer needs to
// be changed, too
curr_bin[i] += extra_points;
if (!colvars[i]->hard_lower_boundary)
if (curr_bin[i] < min_buffer) {
int const extra_points = (min_buffer - curr_bin[i]);
new_lb -= extra_points * colvars[i]->width;
new_size += extra_points;
// changed offset in this direction => the pointer needs to
// be changed, too
curr_bin[i] += extra_points;
changed_lb = true;
cvm::log ("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new lower boundary for colvar \""+
colvars[i]->name+"\", at "+
cvm::to_str (new_lower_boundaries[i])+".\n");
}
changed_lb = true;
cvm::log ("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new lower boundary for colvar \""+
colvars[i]->name+"\", at "+
cvm::to_str (new_lower_boundaries[i])+".\n");
}
if (curr_bin[i] > new_size - min_buffer - 1) {
int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer);
new_ub += extra_points * colvars[i]->width;
new_size += extra_points;
if (!colvars[i]->hard_upper_boundary)
if (curr_bin[i] > new_size - min_buffer - 1) {
int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer);
new_ub += extra_points * colvars[i]->width;
new_size += extra_points;
changed_ub = true;
cvm::log ("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new upper boundary for colvar \""+
colvars[i]->name+"\", at "+
cvm::to_str (new_upper_boundaries[i])+".\n");
}
changed_ub = true;
cvm::log ("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new upper boundary for colvar \""+
colvars[i]->name+"\", at "+
cvm::to_str (new_upper_boundaries[i])+".\n");
}
if (changed_lb || changed_ub)
changed_grids = true;
@ -1521,7 +1523,8 @@ std::ostream & colvarbias_meta::write_restart (std::ostream& os)
void colvarbias_meta::write_pmf()
{
// allocate a new grid to store the pmf
colvar_grid_scalar *pmf = new colvar_grid_scalar (colvars);
colvar_grid_scalar *pmf = new colvar_grid_scalar (*hills_energy);
pmf->create();
std::string fes_file_name_prefix (cvm::output_prefix);
@ -1544,17 +1547,18 @@ void colvarbias_meta::write_pmf()
cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature;
pmf->multiply_constant (well_temper_scale);
}
std::string const fes_file_name (fes_file_name_prefix +
((comm != single_replica) ? ".partial" : "") +
(dump_fes_save ?
"."+cvm::to_str (cvm::step_absolute()) : "") +
".pmf");
cvm::backup_file (fes_file_name.c_str());
std::ofstream fes_os (fes_file_name.c_str());
pmf->write_multicol (fes_os);
fes_os.close();
{
std::string const fes_file_name (fes_file_name_prefix +
((comm != single_replica) ? ".partial" : "") +
(dump_fes_save ?
"."+cvm::to_str (cvm::step_absolute()) : "") +
".pmf");
cvm::backup_file (fes_file_name.c_str());
std::ofstream fes_os (fes_file_name.c_str());
pmf->write_multicol (fes_os);
fes_os.close();
}
}
if (comm != single_replica) {
// output the combined PMF from all replicas
pmf->reset();