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Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH)

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This commit is contained in:
Giacomo Fiorin
2016-10-24 17:11:09 -04:00
parent be2d155cef
commit e02505c8cc
2 changed files with 60 additions and 32 deletions
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84
lib/colvars/colvarbias_meta.cpp
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@ -159,6 +159,23 @@ int colvarbias_meta::init(std::string const &conf)
cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n");
}
// for ebmeta
target_dist = NULL;
get_keyval(conf, "ebMeta", ebmeta, false);
if(ebmeta){
target_dist = new colvar_grid_scalar();
target_dist->init_from_colvars(colvars);
get_keyval(conf, "targetdistfile", target_dist_file);
std::ifstream targetdiststream(target_dist_file.c_str());
target_dist->read_multicol(targetdiststream);
// normalize target distribution and multiply by effective volume = exp(differential entropy)
target_dist->multiply_constant(1.0/target_dist->integral());
cvm::real volume = std::exp(target_dist->entropy());
target_dist->multiply_constant(volume);
get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, 0);
}
if (cvm::debug())
cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
@ -186,6 +203,11 @@ colvarbias_meta::~colvarbias_meta()
if (hills_traj_os.is_open())
hills_traj_os.close();
if(target_dist) {
delete target_dist;
target_dist = NULL;
}
if (cvm::n_meta_biases > 0)
cvm::n_meta_biases -= 1;
}
@ -221,9 +243,7 @@ colvarbias_meta::create_hill(colvarbias_meta::hill const &h)
// output to trajectory (if specified)
if (hills_traj_os.is_open()) {
hills_traj_os << (hills.back()).output_traj();
if (cvm::debug()) {
hills_traj_os.flush();
}
hills_traj_os.flush();
}
has_data = true;
@ -258,8 +278,7 @@ colvarbias_meta::delete_hill(hill_iter &h)
hills_traj_os << "# DELETED this hill: "
<< (hills.back()).output_traj()
<< "\n";
if (cvm::debug())
hills_traj_os.flush();
hills_traj_os.flush();
}
return hills.erase(h);
@ -381,38 +400,37 @@ int colvarbias_meta::update()
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": adding a new hill at step "+cvm::to_str(cvm::step_absolute())+".\n");
cvm::real hills_scale=1.0;
if (ebmeta) {
hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index());
if(cvm::step_absolute() <= ebmeta_equil_steps) {
cvm::real const hills_lambda=(cvm::real(ebmeta_equil_steps - cvm::step_absolute()))/(cvm::real(ebmeta_equil_steps));
hills_scale = hills_lambda + (1-hills_lambda)*hills_scale;
}
}
if (well_tempered) {
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
}
hills_scale *= std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
}
switch (comm) {
case single_replica:
if (well_tempered) {
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
}
cvm::real const exp_weight = std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill(hill((hill_weight*exp_weight), colvars, hill_width));
} else {
create_hill(hill(hill_weight, colvars, hill_width));
}
create_hill(hill(hill_weight*hills_scale, colvars, hill_width));
break;
case multiple_replicas:
if (well_tempered) {
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
}
cvm::real const exp_weight = std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill(hill((hill_weight*exp_weight), colvars, hill_width, replica_id));
} else {
create_hill(hill(hill_weight, colvars, hill_width, replica_id));
}
create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id));
if (replica_hills_os.is_open()) {
replica_hills_os << hills.back();
} else {
@ -1507,7 +1525,9 @@ int colvarbias_meta::setup_output()
("."+replica_id) :
("") )+
".hills.traj");
hills_traj_os.open(traj_file_name.c_str());
if (!hills_traj_os.is_open()) {
hills_traj_os.open(traj_file_name.c_str());
}
if (!hills_traj_os.is_open())
cvm::error("Error: in opening hills output file \"" +
traj_file_name+"\".\n", FILE_ERROR);