| version 1.19 | version 1.20 |
|---|
| |
| cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n"); | 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()) | if (cvm::debug()) |
| cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+ | cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+ |
| ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n"); | ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n"); |
| |
| if (hills_traj_os.is_open()) | if (hills_traj_os.is_open()) |
| hills_traj_os.close(); | hills_traj_os.close(); |
| | |
| | if(target_dist) { |
| | delete target_dist; |
| | target_dist = NULL; |
| | } |
| | |
| if (cvm::n_meta_biases > 0) | if (cvm::n_meta_biases > 0) |
| cvm::n_meta_biases -= 1; | cvm::n_meta_biases -= 1; |
| } | } |
| |
| // output to trajectory (if specified) | // output to trajectory (if specified) |
| if (hills_traj_os.is_open()) { | if (hills_traj_os.is_open()) { |
| hills_traj_os << (hills.back()).output_traj(); | hills_traj_os << (hills.back()).output_traj(); |
| if (cvm::debug()) { | |
| hills_traj_os.flush(); | hills_traj_os.flush(); |
| } | } |
| } | |
| | |
| has_data = true; | has_data = true; |
| return hills.end(); | return hills.end(); |
| |
| hills_traj_os << "# DELETED this hill: " | hills_traj_os << "# DELETED this hill: " |
| << (hills.back()).output_traj() | << (hills.back()).output_traj() |
| << "\n"; | << "\n"; |
| if (cvm::debug()) | |
| hills_traj_os.flush(); | hills_traj_os.flush(); |
| } | } |
| | |
| |
| ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ | ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+ |
| ": adding a new hill at step "+cvm::to_str(cvm::step_absolute())+".\n"); | ": adding a new hill at step "+cvm::to_str(cvm::step_absolute())+".\n"); |
| | |
| switch (comm) { | cvm::real hills_scale=1.0; |
| | |
| case single_replica: | if (ebmeta) { |
| if (well_tempered) { | hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index()); |
| cvm::real hills_energy_sum_here = 0.0; | if(cvm::step_absolute() <= ebmeta_equil_steps) { |
| if (use_grids) { | cvm::real const hills_lambda=(cvm::real(ebmeta_equil_steps - cvm::step_absolute()))/(cvm::real(ebmeta_equil_steps)); |
| std::vector<int> curr_bin = hills_energy->get_colvars_index(); | hills_scale = hills_lambda + (1-hills_lambda)*hills_scale; |
| 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)); | |
| } | } |
| break; | |
| | |
| case multiple_replicas: | |
| if (well_tempered) { | if (well_tempered) { |
| cvm::real hills_energy_sum_here = 0.0; | cvm::real hills_energy_sum_here = 0.0; |
| if (use_grids) { | if (use_grids) { |
| |
| } else { | } else { |
| calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here); | 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())); | hills_scale *= 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)); | |
| } | } |
| | |
| | switch (comm) { |
| | |
| | case single_replica: |
| | |
| | create_hill(hill(hill_weight*hills_scale, colvars, hill_width)); |
| | |
| | break; |
| | |
| | case multiple_replicas: |
| | create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id)); |
| if (replica_hills_os.is_open()) { | if (replica_hills_os.is_open()) { |
| replica_hills_os << hills.back(); | replica_hills_os << hills.back(); |
| } else { | } else { |
| |
| ("."+replica_id) : | ("."+replica_id) : |
| ("") )+ | ("") )+ |
| ".hills.traj"); | ".hills.traj"); |
| | if (!hills_traj_os.is_open()) { |
| hills_traj_os.open(traj_file_name.c_str()); | hills_traj_os.open(traj_file_name.c_str()); |
| | } |
| if (!hills_traj_os.is_open()) | if (!hills_traj_os.is_open()) |
| cvm::error("Error: in opening hills output file \"" + | cvm::error("Error: in opening hills output file \"" + |
| traj_file_name+"\".\n", FILE_ERROR); | traj_file_name+"\".\n", FILE_ERROR); |