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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13126 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-02-19 18:20:52 +00:00
parent f300f2367e
commit 067833cf07
21 changed files with 597 additions and 360 deletions
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18
lib/colvars/colvarbias_meta.cpp
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@ -86,7 +86,7 @@ colvarbias_meta::colvarbias_meta(std::string const &conf, char const *key)
colvars[i]->enable(colvar::task_grid);
}
hills_energy = new colvar_grid_scalar (colvars);
hills_energy = new colvar_grid_scalar(colvars);
hills_energy_gradients = new colvar_grid_gradient(colvars);
} else {
rebin_grids = false;
@ -430,11 +430,11 @@ cvm::real colvarbias_meta::update()
new_hills_energy->lower_boundaries = new_lower_boundaries;
new_hills_energy->upper_boundaries = new_upper_boundaries;
new_hills_energy->create(new_sizes, 0.0, 1);
new_hills_energy->setup(new_sizes, 0.0, 1);
new_hills_energy_gradients->lower_boundaries = new_lower_boundaries;
new_hills_energy_gradients->upper_boundaries = new_upper_boundaries;
new_hills_energy_gradients->create(new_sizes, 0.0, colvars.size());
new_hills_energy_gradients->setup(new_sizes, 0.0, colvars.size());
new_hills_energy->map_grid(*hills_energy);
new_hills_energy_gradients->map_grid(*hills_energy_gradients);
@ -746,6 +746,8 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
break;
case colvarvalue::type_notset:
case colvarvalue::type_all:
default:
break;
}
}
@ -959,7 +961,7 @@ void colvarbias_meta::update_replicas_registry()
(replicas.back())->comm = multiple_replicas;
if (use_grids) {
(replicas.back())->hills_energy = new colvar_grid_scalar (colvars);
(replicas.back())->hills_energy = new colvar_grid_scalar(colvars);
(replicas.back())->hills_energy_gradients = new colvar_grid_gradient(colvars);
}
}
@ -1552,7 +1554,7 @@ void colvarbias_meta::write_pmf()
{
// allocate a new grid to store the pmf
colvar_grid_scalar *pmf = new colvar_grid_scalar(*hills_energy);
pmf->create();
pmf->setup();
std::string fes_file_name_prefix(cvm::output_prefix);
@ -1582,7 +1584,7 @@ void colvarbias_meta::write_pmf()
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
cvm::backup_file(fes_file_name.c_str());
std::ofstream fes_os(fes_file_name.c_str());
cvm::ofstream fes_os(fes_file_name.c_str());
pmf->write_multicol(fes_os);
fes_os.close();
}
@ -1606,7 +1608,7 @@ void colvarbias_meta::write_pmf()
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
cvm::backup_file(fes_file_name.c_str());
std::ofstream fes_os(fes_file_name.c_str());
cvm::ofstream fes_os(fes_file_name.c_str());
pmf->write_multicol(fes_os);
fes_os.close();
}
@ -1621,7 +1623,7 @@ void colvarbias_meta::write_replica_state_file()
// write down also the restart for the other replicas: TODO: this
// is duplicated code, that could be cleaned up later
cvm::backup_file(replica_state_file.c_str());
std::ofstream rep_state_os(replica_state_file.c_str());
cvm::ofstream rep_state_os(replica_state_file.c_str());
if (!rep_state_os.good())
cvm::fatal_error("Error: in opening file \""+
replica_state_file+"\" for writing.\n");