Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH) (e02505c8) · Commits · 郑智淋 / lammps

lib/colvars/colvarbias_meta.cpp

+52 −32

Original line number	Diff line number	Diff line
		@@ -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;
		}
		@@ -221,10 +243,8 @@ 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();
		}
		}

		has_data = true;
		return hills.end();
		@@ -258,7 +278,6 @@ 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();
		}

		@@ -381,25 +400,16 @@ int colvarbias_meta::update()
		((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
		": 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 (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);
		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;
		}
		cvm::real const exp_weight = std::exp(-1.0hills_energy_sum_here/(bias_temperaturecvm::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) {
		cvm::real hills_energy_sum_here = 0.0;
		if (use_grids) {
		@@ -408,11 +418,19 @@ int colvarbias_meta::update()
		} else {
		calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
		}
		cvm::real const exp_weight = std::exp(-1.0hills_energy_sum_here/(bias_temperaturecvm::boltzmann()));
		create_hill(hill((hill_weight*exp_weight), colvars, hill_width, replica_id));
		} else {
		create_hill(hill(hill_weight, colvars, hill_width, replica_id));
		hills_scale = std::exp(-1.0hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
		}

		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()) {
		replica_hills_os << hills.back();
		} else {
		@@ -1507,7 +1525,9 @@ int colvarbias_meta::setup_output()
		("."+replica_id) :
		("") )+
		".hills.traj");
		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);

lib/colvars/colvarbias_meta.h

+8 −0

Original line number	Diff line number	Diff line
		@@ -147,6 +147,14 @@ protected:
		/// \brief Biasing temperature in well-tempered metadynamics
		cvm::real bias_temperature;

		// EBmeta parameters
		bool ebmeta;
		colvar_grid_scalar* target_dist;
		std::string target_dist_file;
		cvm::real target_dist_volume;
		size_t ebmeta_equil_steps;


		/// \brief Try to read the restart information by allocating new
		/// grids before replacing the current ones (used e.g. in
		/// multiple_replicas)

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