colvarbias_meta Class Reference

Metadynamics bias (implementation of ). More...

#include <colvarbias_meta.h>

Inheritance diagram for colvarbias_meta:

List of all members.

Public Types
typedef std::list< hill >::iterator	hill_iter
enum	Communication { single_replica, multiple_replicas }
	Communication between different replicas. More...
Public Member Functions
	colvarbias_meta (std::string const &conf, char const *key)
	Constructor.
virtual	~colvarbias_meta ()
	Destructor.
virtual void	update ()
	Retrieve colvar values and calculate their biasing forces.
virtual void	analyse ()
	Perform analysis.
virtual std::istream &	read_restart (std::istream &is)
	Read the bias configuration from a restart file.
virtual std::ostream &	write_restart (std::ostream &os)
	Write the bias configuration to a restart file.
Public Attributes
Communication	comm
	Communication between different replicas.
Protected Member Functions
void	recount_hills_off_grid (hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge)
	Regenerate the hills_off_grid list.
std::istream &	read_hill (std::istream &is)
	Read a hill from a file.
virtual std::list< hill >::const_iterator	create_hill (hill const &h)
	Add a new hill; if a .hills trajectory is written, write it there; if there is more than one replica, communicate it to the others.
virtual std::list< hill >::const_iterator	delete_hill (std::list< hill >::iterator &h)
	Remove a previously saved hill (returns an iterator for the next hill in the list).
virtual void	calc_hills (hill_iter h_first, hill_iter h_last, cvm::real &energy, std::vector< colvarvalue > const &values=std::vector< colvarvalue >(0))
	Calculate the values of the hills, incrementing colvar_energy.
virtual void	calc_hills_force (size_t const &i, hill_iter h_first, hill_iter h_last, std::vector< colvarvalue > &forces, std::vector< colvarvalue > const &values=std::vector< colvarvalue >(0))
	Calculate the forces acting on the i-th colvar, incrementing colvar_forces[i]; must be called after calc_hills each time the values of the colvars are changed.
void	project_hills (hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge, colvar_grid_gradient *gf, cvm::real const scale_factor=1.0)
	Project the selected hills onto grids.
virtual void	register_replica_file (std::string const &new_file)
	Add this replica to the registry (called only when != ).
virtual void	update_replica_files_registry ()
	Read the names all replica output files which have been added, skipping the one which is currently being written to (called only when != ).
virtual void	read_replica_files ()
	Read new data from replicas' files (called only when != ).
Protected Attributes
std::list< hill >	hills
	Parse analysis tasks and options List of hills used on this bias (total); if a grid is employed, these don't need to be updated at every time step.
hill_iter	new_hills_begin
	Iterator to the first of the "newest" hills (when using grids, those who haven't been mapped yet).
std::list< hill >	hills_off_grid
	List of hills used on this bias that are on the boundary edges; these are updated regardless of whether hills are used.
hill_iter	new_hills_off_grid_begin
	Same as new_hills_begin, but for the off-grid ones.
cvm::real	hill_weight
	Height of new hills.
bool	use_grids
	Bin the hills on grids of energy and forces, and use them to force the colvars (as opposed to deriving the hills analytically).
bool	rebin_grids
	Rebin the hills upon restarting.
bool	expand_grids
	Should the grids be expanded if necessary?
size_t	grids_freq
	How often the hills should be projected onto the grids.
bool	keep_hills
	Whether to keep the hills in the restart file (e.g. to do meaningful accurate rebinning afterwards).
bool	dump_fes
	Dump the free energy surface (.pmf file) every restartFrequency.
bool	dump_fes_save
	Keep the free energy surface files at different iterations, appending a step number to each.
colvar_grid_scalar *	hills_energy
	Hill energy, cached on a grid.
colvar_grid_gradient *	hills_energy_gradients
	Hill forces, cached on a grid.
cvm::real	hill_width
	width of a hill
size_t	new_hill_freq
	Number of simulation steps between two hills.
bool	b_hills_traj
	Write the hill logfile.
std::ofstream	hills_traj_os
	Logfile of hill management (creation and deletion).
std::string	replica
	Identifier for this replica.
size_t	replica_update_freq
	Frequency at which output files from other replicas are checked.
std::string	replica_files_registry
	List of hill files from all the replicas.
std::list< std::string >	replica_files
	Replicas file names.
std::list< size_t >	replica_files_pos
	Positions in replica files (files are reopened at these positions).
std::ofstream	replica_out_file
	File to contain the hills created by this replica in this run.
std::string	replica_out_file_name
	File to contain the hills created by this replica in this run (name).
size_t	free_energy_begin
	Select only hills after this step.
size_t	free_energy_end
	Select only hills before this step.
bool	shift_fes
	Make the free energy surface be larger than or equal to zero.
cvm::real	free_energy_offset
	Subtract this value from the free energy (after.
std::string	free_energy_file
	Free energy surface output file.
std::string	free_energy_gradients_file
	Free energy gradients output file.
std::string	boltzmann_weights_file
	Boltzmann weights output file.
std::string	boltzmann_counts_file
	Boltzmann counts output file.
cvm::real	boltzmann_weights_scale
	Multiply the exponential weights by this constant.
cvm::real	boltzmann_weights_temp
	Temperature (in K) for Boltzmann weights.
colvar_grid_scalar *	free_energy
	Free energy values.
colvar_grid_gradient *	free_energy_gradients
	Free energy gradients.
colvar_grid_scalar *	boltzmann_weights
	Boltzmann populations (real version).
colvar_grid_count *	boltzmann_counts
	Boltzmann populations (integer version).

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Detailed Description

Metadynamics bias (implementation of ).

Definition at line 13 of file colvarbias_meta.h.

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Member Typedef Documentation

typedef std::list<hill>::iterator colvarbias_meta::hill_iter

Definition at line 44 of file colvarbias_meta.h. Referenced by calc_hills(), calc_hills_force(), create_hill(), read_hill(), and recount_hills_off_grid().

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Member Enumeration Documentation

enum colvarbias_meta::Communication

Communication between different replicas. Enumeration values: single_replica  One replica (default). multiple_replicas  Hills added concurrently by several replicas. Definition at line 18 of file colvarbias_meta.h. { single_replica, multiple_replicas };

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Constructor & Destructor Documentation

colvarbias_meta::colvarbias_meta (  std::string const &  conf, char const *  key )

Constructor. Definition at line 26 of file colvarbias_meta.C. References b_hills_traj, comm, colvarmodule::debug(), dump_fes, dump_fes_save, expand_grids, colvarmodule::fatal_error(), GETCWD, grids_freq, hill_weight, hill_width, hills_energy, hills_energy_gradients, hills_traj_os, keep_hills, colvarmodule::log(), new_hill_freq, PATHSEP, PI, rebin_grids, register_replica_file(), replica, replica_files_registry, replica_out_file, replica_out_file_name, replica_update_freq, single_replica, and use_grids. : colvarbias (conf, key), comm (single_replica), new_hills_begin (hills.end()) // free_energy (NULL), free_energy_gradients (NULL), // boltzmann_weights (NULL), boltzmann_counts (NULL) { if (cvm::n_abf_biases > 0) cvm::log ("Warning: ABF and metadynamics running at the " "same time can give inconsistent results.\n"); get_keyval (conf, "hillWeight", hill_weight, 0.1); if (hill_weight == 0.0) cvm::log ("Warning: zero weight specified, " "this bias will have no effect.\n"); get_keyval (conf, "newHillFrequency", new_hill_freq, 1000); get_keyval (conf, "hillWidth", hill_width, ::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 && (comm != single_replica)) { cvm::log ("Warning: calculations with a grid and " "multiple replicas is currently not supported: " "setting useGrids to \"no\".\n"); use_grids = false; } if (use_grids) { get_keyval (conf, "gridsUpdateFrequency", grids_freq, new_hill_freq); get_keyval (conf, "rebinGrids", rebin_grids, false); expand_grids = false; for (size_t i = 0; i < colvars.size(); i++) { if (colvars[i]->expand_boundaries) { expand_grids = true; cvm::log ("Will expand the metadynamics grid when the colvar \""+ colvars[i]->name+"\" approaches the boundaries.\n"); } } // get_keyval (conf, "expandGrids", expand_grids, false); get_keyval (conf, "keepHills", keep_hills, false); get_keyval (conf, "dumpFreeEnergyFile", dump_fes, true); get_keyval (conf, "saveFreeEnergyFile", dump_fes_save, false); for (size_t i = 0; i < colvars.size(); i++) { colvars[i]->enable (colvar::task_grid); } hills_energy = new colvar_grid_scalar (colvars); hills_energy_gradients = new colvar_grid_gradient (colvars); } if (comm != single_replica) { get_keyval (conf, "replicaID", replica, std::string ("")); if (!replica.size()) cvm::fatal_error ("Error: you must define an id for this replica " "when using more than one.\n"); get_keyval (conf, "replicaFilesRegistry", replica_files_registry, (this->name+".replica_files.txt")); get_keyval (conf, "replicaUpdateFrequency", replica_update_freq, new_hill_freq); char *pwd = new char[321]; if (GETCWD (pwd, 320) == NULL) cvm::fatal_error ("Error: cannot read the current working directory.\n"); replica_out_file_name = (std::string (pwd)+std::string (PATHSEP)+ cvm::output_prefix+".colvars."+this->name+ "."+replica+".hills"); delete pwd; replica_out_file.open (replica_out_file_name.c_str()); if (!replica_out_file.good()) cvm::fatal_error ("Error: in opening hills output file \""+ replica_out_file_name+"\".\n"); register_replica_file (replica_out_file_name); } get_keyval (conf, "writeHillsTrajectory", b_hills_traj, false); if (b_hills_traj) { std::string const traj_file_name (cvm::output_prefix+ ".colvars."+this->name+ ( (comm != single_replica) ? ("."+replica) : ("") )+ ".hills.traj"); hills_traj_os.open (traj_file_name.c_str()); if (!hills_traj_os.good()) cvm::fatal_error ("Error: in opening hills output file \"" + traj_file_name + "\".\n"); } if (cvm::debug()) cvm::log ("Done initializing the metadynamics bias \""+this->name+"\".\n"); save_delimiters = false; }

colvarbias_meta::~colvarbias_meta (   )  [virtual]

Destructor. Definition at line 200 of file colvarbias_meta.C. References hills_energy, hills_energy_gradients, hills_traj_os, and replica_out_file. { if (hills_energy) { delete hills_energy; hills_energy = NULL; } if (hills_energy_gradients) { delete hills_energy_gradients; hills_energy_gradients = NULL; } // if (free_energy) { // delete free_energy; // free_energy = NULL; // } // if (free_energy_gradients) { // delete free_energy_gradients; // free_energy_gradients = NULL; // } // if (boltzmann_weights) { // delete boltzmann_weights; // boltzmann_weights = NULL; // } // if (boltzmann_counts) { // delete boltzmann_counts; // boltzmann_counts = NULL; // } if (replica_out_file.good()) replica_out_file.close(); if (hills_traj_os.good()) hills_traj_os.close(); }

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Member Function Documentation

void colvarbias_meta::analyse (   )  [virtual]

Perform analysis. Reimplemented from colvarbias. Definition at line 1180 of file colvarbias_meta.C. {}

void colvarbias_meta::calc_hills (  hill_iter  h_first, hill_iter  h_last, cvm::real &  energy, std::vector< colvarvalue > const &  values = std::vector< colvarvalue >(0) )  [protected, virtual]

Calculate the values of the hills, incrementing colvar_energy. Definition at line 525 of file colvarbias_meta.C. References hill_iter, colvar_grid< T >::value(), and colvar_grid< T >::widths. Referenced by project_hills(), and update(). { std::vector<colvarvalue> curr_values (colvars.size()); for (size_t i = 0; i < colvars.size(); i++) { curr_values[i].type (colvars[i]->type()); } if (colvar_values.size()) { for (size_t i = 0; i < colvars.size(); i++) { curr_values[i] = colvar_values[i]; } } else { for (size_t i = 0; i < colvars.size(); i++) { curr_values[i] = colvars[i]->value(); } } for (hill_iter h = h_first; h != h_last; h++) { // compute the gaussian exponent cvm::real cv_sqdev = 0.0; for (size_t i = 0; i < colvars.size(); i++) { colvarvalue const &x = curr_values[i]; colvarvalue const &center = h->centers[i]; cvm::real const half_width = 0.5 * h->widths[i]; cv_sqdev += (colvars[i]->dist2 (x, center)) / (half_width*half_width); } // compute the gaussian if (cv_sqdev > 23.0) { // set it to zero if the exponent is more negative than log(1.0E-05) h->value (0.0); } else { h->value (::exp (-0.5*cv_sqdev)); } energy += h->energy(); } }

void colvarbias_meta::calc_hills_force (  size_t const &  i, hill_iter  h_first, hill_iter  h_last, std::vector< colvarvalue > &  forces, std::vector< colvarvalue > const &  values = std::vector< colvarvalue >(0) )  [protected, virtual]

Calculate the forces acting on the i-th colvar, incrementing colvar_forces[i]; must be called after calc_hills each time the values of the colvars are changed. Definition at line 568 of file colvarbias_meta.C. References hill_iter. Referenced by project_hills(), and update(). { // Retrieve the value of the colvar colvarvalue x (values.size() ? values[i].type() : colvars[i]->type()); x = (values.size() ? values[i] : colvars[i]->value()); // do the type check only once (all colvarvalues in the hills series // were already saved with their types matching those in the // colvars) switch (colvars[i]->type()) { case colvarvalue::type_scalar: for (hill_iter h = h_first; h != h_last; h++) { if (h->value() == 0.0) continue; colvarvalue const &center = h->centers[i]; cvm::real const half_width = 0.5 * h->widths[i]; forces[i].real_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * (colvars[i]->dist2_lgrad (x, center)).real_value ); } break; case colvarvalue::type_vector: case colvarvalue::type_unitvector: for (hill_iter h = h_first; h != h_last; h++) { if (h->value() == 0.0) continue; colvarvalue const &center = h->centers[i]; cvm::real const half_width = 0.5 * h->widths[i]; forces[i].rvector_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * (colvars[i]->dist2_lgrad (x, center)).rvector_value ); } break; case colvarvalue::type_quaternion: for (hill_iter h = h_first; h != h_last; h++) { if (h->value() == 0.0) continue; colvarvalue const &center = h->centers[i]; cvm::real const half_width = 0.5 * h->widths[i]; forces[i].quaternion_value += ( h->weight() * h->value() * (0.5 / (half_width*half_width)) * (colvars[i]->dist2_lgrad (x, center)).quaternion_value ); } break; case colvarvalue::type_notset: break; } }

std::list< colvarbias_meta::hill >::const_iterator colvarbias_meta::create_hill (  hill const &  h  )  [protected, virtual]

Add a new hill; if a .hills trajectory is written, write it there; if there is more than one replica, communicate it to the others. Definition at line 246 of file colvarbias_meta.C. References colvar_grid< T >::bin_distance_from_boundaries(), colvarbias_meta::hill::centers, comm, colvarmodule::debug(), colvarmodule::fatal_error(), hill_iter, hills, hills_energy, hills_off_grid, hills_traj_os, new_hills_begin, replica, and replica_out_file. Referenced by update(). { hill_iter const hills_end = hills.end(); hills.push_back (h); if (new_hills_begin == hills_end) { // set the beginning of the "new" hills new_hills_begin = hills.end(); new_hills_begin--; } if (use_grids) { // also add it to the list of hills that are off-grid, which // receive special treatment (i.e. they are computed analytically) cvm::real const min_dist = hills_energy->bin_distance_from_boundaries (h.centers); if (min_dist < (3.0 * ::floor (hill_width)) + 1.0) { hills_off_grid.push_back (hills.back()); } } // output to trajectory if (hills_traj_os.good()) { hills_traj_os << (hills.back()).output_traj(); if (cvm::debug()) { hills_traj_os.flush(); } } // output to the replica file if (comm != single_replica) { if (replica_out_file.good()) { replica_out_file << hills.back(); } else { cvm::fatal_error ("Error in writing to the hills database for replica \""+ replica+"\".\n"); } } return hills.end(); }

virtual std::list<hill>::const_iterator colvarbias_meta::delete_hill (  std::list< hill >::iterator &  h  )  [protected, virtual]

Remove a previously saved hill (returns an iterator for the next hill in the list).

void colvarbias_meta::project_hills (  hill_iter  h_first, hill_iter  h_last, colvar_grid_scalar *  ge, colvar_grid_gradient *  gf, cvm::real const   scale_factor = 1.0 )  [protected]

Project the selected hills onto grids. Definition at line 1115 of file colvarbias_meta.C. References colvar_grid_gradient::acc_force(), colvar_grid_scalar::acc_value(), colvar_grid< T >::bin_to_value_scalar(), calc_hills(), calc_hills_force(), colvarmodule::debug(), hills, hills_energy, colvar_grid< T >::incr(), colvar_grid< T >::index_ok(), colvarmodule::log(), and colvar_grid< T >::new_index(). Referenced by read_restart(), and update(). { if (cvm::debug()) cvm::log ("Projecting hills.\n"); std::vector<colvarvalue> colvar_values (colvars.size()); std::vector<cvm::real> colvar_forces_scalar (colvars.size()); std::vector<int> he_ix = he->new_index(); std::vector<int> hg_ix = (hg != NULL) ? hg->new_index() : std::vector<int> (0); cvm::real hills_energy_here = 0.0; std::vector<colvarvalue> hills_forces_here (colvars.size(), 0.0); // loop over the points of the grid for ( ; he->index_ok (he_ix) && ((hg != NULL) ? hg->index_ok (hg_ix) : true); ) { for (size_t i = 0; i < colvars.size(); i++) { colvar_values[i] = hills_energy->bin_to_value_scalar (he_ix[i], i); } // loop over the hills and increment the energy grid locally hills_energy_here = 0.0; calc_hills (h_first, h_last, hills_energy_here, colvar_values); he->acc_value (he_ix, scale_factor * hills_energy_here); if (hg != NULL) { for (size_t i = 0; i < colvars.size(); i++) { hills_forces_here[i].reset(); calc_hills_force (i, h_first, h_last, hills_forces_here, colvar_values); colvar_forces_scalar[i] = scale_factor * hills_forces_here[i].real_value; } hg->acc_force (hg_ix, &(colvar_forces_scalar.front())); } he->incr (he_ix); if (hg != NULL) hg->incr (hg_ix); } if (! keep_hills) { hills.erase (hills.begin(), hills.end()); } }

std::istream & colvarbias_meta::read_hill (  std::istream &  is  )  [protected]

Read a hill from a file. Definition at line 904 of file colvarbias_meta.C. References colvar_grid< T >::bin_distance_from_boundaries(), comm, hill_iter, hill_weight, hills, hills_energy, hills_off_grid, colvarparse::key_lookup(), new_hills_begin, and replica. Referenced by read_replica_files(), and read_restart(). { if (!is) return is; // do nothing if failbit is set size_t const start_pos = is.tellg(); std::string data; if ( !(is >> read_block ("hill", data)) ) { is.clear(); is.seekg (start_pos, std::ios::beg); is.setstate (std::ios::failbit); return is; } std::string h_replica = ""; int h_it; get_keyval (data, "step", h_it, 0, parse_silent); cvm::real h_weight; get_keyval (data, "weight", h_weight, hill_weight, parse_silent); std::vector<colvarvalue> h_centers (colvars.size()); for (size_t i = 0; i < colvars.size(); i++) { h_centers[i].type ((colvars[i]->value()).type()); } { // it is safer to read colvarvalue objects one at a time; XXX // todo: check to remove it later std::string centers_input; key_lookup (data, "centers", centers_input); std::istringstream centers_is (centers_input); for (size_t i = 0; i < colvars.size(); i++) { centers_is >> h_centers[i]; } } std::vector<cvm::real> h_widths (colvars.size()); get_keyval (data, "widths", h_widths, std::vector<cvm::real> (colvars.size(), 1.0), parse_silent); if (comm != single_replica) get_keyval (data, "replica", h_replica, replica, parse_silent); hill_iter const hills_end = hills.end(); hills.push_back (hill (h_it, h_weight, h_centers, h_widths, h_replica)); if (new_hills_begin == hills_end) { // set the beginning of the "new" hills new_hills_begin = hills.end(); new_hills_begin--; } if (use_grids) { // add this also to the list of hills that are off-grid, which will // be computed analytically cvm::real const min_dist = hills_energy->bin_distance_from_boundaries ((hills.back()).centers); if (min_dist < (3.0 * ::floor (hill_width)) + 1.0) { hills_off_grid.push_back (hills.back()); } } return is; }

void colvarbias_meta::read_replica_files (   )  [protected, virtual]

Read new data from replicas' files (called only when != ). Definition at line 705 of file colvarbias_meta.C. References colvarmodule::debug(), colvarmodule::fatal_error(), hills, hills_traj_os, colvarmodule::log(), read_hill(), replica_files, replica_files_pos, and colvarmodule::to_str(). Referenced by read_restart(), and update(). { // read hills from the other replicas' files; for each file, resume // the position recorded last time std::list<std::string>::iterator rsi = replica_files.begin(); std::list<size_t>::iterator pi = replica_files_pos.begin(); for ( ; rsi != replica_files.end(); pi++, rsi++) { if (cvm::debug()) cvm::log ("Checking for new hills in the replica file \""+ (*rsi)+"\".\n"); std::ifstream is ((*rsi).c_str()); if (is.good()) { is.seekg ((*pi), std::ios::beg); while (read_hill (is)) { if (cvm::debug()) cvm::log ("Read a previously saved hill under the " "metadynamics bias \""+ this->name+"\", created by replica "+ (hills.back()).replica+ " at step "+ cvm::to_str ((hills.back()).it)+".\n"); // output to trajectory if (hills_traj_os.good()) { hills_traj_os << (hills.back()).output_traj(); if (cvm::debug()) { hills_traj_os.flush(); } } } is.clear(); // store it for the next read *pi = is.tellg(); if (cvm::debug()) cvm::log ("Stopped reading at position "+ cvm::to_str (*pi)+".\n"); } else { cvm::fatal_error ("Error: cannot read from file \""+(*rsi)+"\".\n"); } is.close(); } }

std::istream & colvarbias_meta::read_restart (  std::istream &  is  )  [virtual]

Read the bias configuration from a restart file. Implements colvarbias. Definition at line 760 of file colvarbias_meta.C. References comm, colvarmodule::debug(), colvarmodule::fatal_error(), hills, hills_energy, hills_energy_gradients, keep_hills, colvarmodule::log(), colvar_grid< T >::map_grid(), new_hills_begin, project_hills(), read_hill(), read_replica_files(), colvar_grid_gradient::read_restart(), colvar_grid_scalar::read_restart(), recount_hills_off_grid(), and update_replica_files_registry(). { size_t const start_pos = is.tellg(); cvm::log ("Restarting metadynamics bias \""+ this->name+"\".\n"); std::string key, brace, conf; if ( !(is >> key) || !(key == "metadynamics") || !(is >> brace) || !(brace == "{") || !(is >> colvarparse::read_block ("configuration", conf)) ) { cvm::log ("Error: in reading restart configuration for metadynamics bias \""+ this->name+"\" at position "+ cvm::to_str (start_pos)+" in stream.\n"); is.clear(); is.seekg (start_pos, std::ios::beg); is.setstate (std::ios::failbit); return is; } std::string name = ""; if ( colvarparse::get_keyval (conf, "name", name, std::string (""), colvarparse::parse_silent) && (name != this->name) ) cvm::fatal_error ("Error: in the restart file, the " "\"metadynamics\" block has a wrong name: different system?\n"); if (name.size() == 0) { cvm::fatal_error ("Error: \"metadynamics\" block in the restart file " "has no identifiers.\n"); } if (this->comm == single_replica) { if (use_grids) { if (expand_grids) { // the boundaries of the colvars may have been changed (note: // this second reallocation may be deleted when the new // restart format for the grids has kicked in) delete hills_energy; delete hills_energy_gradients; hills_energy = new colvar_grid_scalar (colvars); hills_energy_gradients = new colvar_grid_gradient (colvars); } if ( !(is >> key) || !(key == std::string ("hills_energy")) || !(hills_energy->read_restart (is)) ) { cvm::log ("Error: in reading restart information for metadynamics bias \""+ this->name+"\".\n"); is.clear(); is.seekg (start_pos, std::ios::beg); is.setstate (std::ios::failbit); return is; } if ( !(is >> key) || !(key == std::string ("hills_energy_gradients")) || !(hills_energy_gradients->read_restart (is)) ) { cvm::log ("Error: in reading restart information for metadynamics bias \""+ this->name+"\".\n"); is.clear(); is.seekg (start_pos, std::ios::beg); is.setstate (std::ios::failbit); return is; } } // read the hills explicitly (if there are any) while (this->read_hill (is)) { if (cvm::debug()) cvm::log ("Read a previously saved hill under the " "metadynamics bias \""+ this->name+"\", created at step "+ cvm::to_str ((hills.back()).it)+".\n"); } is.clear(); new_hills_begin = hills.end(); if (rebin_grids) { // allocate new grids, based on the CURRENT boundaries and // widths, as per the restarts, and project the grids from the // restart file onto them colvar_grid_scalar *new_hills_energy = new colvar_grid_scalar (colvars); colvar_grid_gradient *new_hills_energy_gradients = new colvar_grid_gradient (colvars); if (keep_hills && (hills.size() > 0)) { // if there are hills, recompute the new grids from them cvm::log ("rebinGrids and keepHills defined, recomputing " "analytically the energy and force grids; this may take a while...\n"); project_hills (hills.begin(), hills.end(), new_hills_energy, new_hills_energy_gradients); cvm::log ("rebinning done.\n"); } else { // otherwise, use the grids in the restart file cvm::log ("rebinGrids defined, mapping energy and forces grid to new grids.\n"); new_hills_energy->map_grid (*hills_energy); new_hills_energy_gradients->map_grid (*hills_energy_gradients); } delete hills_energy; delete hills_energy_gradients; hills_energy = new_hills_energy; hills_energy_gradients = new_hills_energy_gradients; if (hills.size()) recount_hills_off_grid (hills.begin(), hills.end(), hills_energy); } } else { // read all hills from the replica files cvm::log ("Multiple replicas have been defined for the " "metadynamics bias \""+this->name+"\", skipping " "the restart file and reading hills from the replica " "files, whose list is contained in \""+ this->replica_files_registry+"\".\n"); this->update_replica_files_registry(); this->read_replica_files(); } is >> brace; if (brace != "}") { cvm::fatal_error ("Error: corrupted restart information for metadynamics bias \""+ this->name+"\": no matching brace at position "+ cvm::to_str (is.tellg())+" in the restart file.\n"); is.setstate (std::ios::failbit); } if (cvm::debug()) cvm::log ("colvarbias_meta::read_restart() done\n"); return is; }

void colvarbias_meta::recount_hills_off_grid (  hill_iter  h_first, hill_iter  h_last, colvar_grid_scalar *  ge )  [protected]

Regenerate the hills_off_grid list. Definition at line 1165 of file colvarbias_meta.C. References colvar_grid< T >::bin_distance_from_boundaries(), hill_iter, hills_energy, and hills_off_grid. Referenced by read_restart(). { hills_off_grid.clear(); for (hill_iter h = h_first; h != h_last; h++) { cvm::real const min_dist = hills_energy->bin_distance_from_boundaries (h->centers); if (min_dist < (3.0 * ::floor (hill_width)) + 1.0) { hills_off_grid.push_back (*h); } } }

void colvarbias_meta::register_replica_file (  std::string const &  new_file  )  [protected, virtual]

Add this replica to the registry (called only when != ). Definition at line 629 of file colvarbias_meta.C. References replica_files_registry. Referenced by colvarbias_meta(). { std::ifstream reg_is (replica_files_registry.c_str()); if (reg_is.good()) { std::string s; while (reg_is >> s) if (new_file == s) { // already found this replica in registry return; } } reg_is.close(); std::ofstream reg_os (replica_files_registry.c_str(), std::ios::app); reg_os << new_file << "\n"; reg_os.close(); }

void colvarbias_meta::update (   )  [virtual]

Retrieve colvar values and calculate their biasing forces. Implements colvarbias. Definition at line 323 of file colvarbias_meta.C. References calc_hills(), calc_hills_force(), comm, colvar_grid< T >::create(), create_hill(), colvarmodule::debug(), colvar_grid< T >::get_colvars_index(), hill_weight, hill_width, hills, hills_energy, hills_energy_gradients, hills_off_grid, colvar_grid< T >::index_ok(), colvarmodule::log(), colvar_grid< T >::lower_boundaries, colvar_grid< T >::map_grid(), multiple_replicas, new_hills_begin, project_hills(), read_replica_files(), replica, replica_out_file, single_replica, colvar_grid< T >::sizes(), colvarmodule::step_relative(), update_replica_files_registry(), colvar_grid< T >::upper_boundaries, and colvar_grid< T >::value(). { if (cvm::debug()) cvm::log ("Updating the metadynamics bias \""+this->name+"\".\n"); if (use_grids) { std::vector<int> curr_bin = hills_energy->get_colvars_index(); if (expand_grids) { // first of all, expand the grids, if specified if (cvm::debug()) cvm::log ("Current coordinates on the grid: "+ cvm::to_str (curr_bin)+".\n"); if (cvm::debug()) cvm::log ("Checking if the grid is big enough.\n"); bool changed_grids = false; int const min_buffer = (3 * (size_t) ::floor (hill_width)) + 1; std::vector<int> new_sizes (hills_energy->sizes()); std::vector<colvarvalue> new_lower_boundaries (hills_energy->lower_boundaries); std::vector<colvarvalue> new_upper_boundaries (hills_energy->upper_boundaries); for (size_t i = 0; i < colvars.size(); i++) { if (! colvars[i]->expand_boundaries) continue; cvm::real &new_lb = new_lower_boundaries[i].real_value; cvm::real &new_ub = new_upper_boundaries[i].real_value; 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; changed_lb = true; cvm::log ("Metadynamics"+((cvm::n_meta_biases > 1) ? " \""+name+"\"" : "")+ ": 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; changed_ub = true; cvm::log ("Metadynamics"+((cvm::n_meta_biases > 1) ? " \""+name+"\"" : "")+ ": 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; } if (changed_grids) { // map everything into new grids if (cvm::debug()) cvm::log ("Expanding the grids for the metadynamics bias \""+ name+"\".\n"); colvar_grid_scalar *new_hills_energy = new colvar_grid_scalar (*hills_energy); colvar_grid_gradient *new_hills_energy_gradients = new colvar_grid_gradient (*hills_energy_gradients); // supply new boundaries to the new grids 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_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->map_grid (*hills_energy); new_hills_energy_gradients->map_grid (*hills_energy_gradients); delete hills_energy; delete hills_energy_gradients; hills_energy = new_hills_energy; hills_energy_gradients = new_hills_energy_gradients; curr_bin = hills_energy->get_colvars_index(); if (cvm::debug()) cvm::log ("Coordinates on the new grid: "+ cvm::to_str (curr_bin)+".\n"); } } } // add a new hill if the required time interval has passed if ((cvm::it % new_hill_freq) == 0) { if (cvm::debug()) cvm::log ("Adding a new hill under the bias \""+ this->name+"\", at step "+cvm::to_str (cvm::it)+".\n"); switch (comm) { case single_replica: create_hill (hill (hill_weight, colvars, hill_width)); break; case multiple_replicas: create_hill (hill (hill_weight, colvars, hill_width, replica)); break; } } // syncronise with the other replicas if specified if (comm != single_replica) { if ((cvm::it % replica_update_freq) == 0) { // the buffer should be always emptied to keep the other // replicas as much in sync as possible replica_out_file.flush(); // read all replica files, except those for this replica; hills // from previous run were already loaded in memory by restarts update_replica_files_registry(); read_replica_files(); } } // calculate the biasing energy and forces colvar_energy = 0.0; for (size_t i = 0; i < colvars.size(); i++) { colvar_forces[i].reset(); } if (use_grids) { // get the forces from the grid if ((cvm::step_relative() % grids_freq) == 0) { // map the most recent gaussians to the grids project_hills (new_hills_begin, hills.end(), hills_energy, hills_energy_gradients); new_hills_begin = hills.end(); } std::vector<int> curr_bin = hills_energy->get_colvars_index(); if (cvm::debug()) cvm::log ("Current coordinates on the grid: "+ cvm::to_str (curr_bin)+".\n"); if (hills_energy->index_ok (curr_bin)) { // within the grid: add the energy and the forces from there colvar_energy += hills_energy->value (curr_bin); for (size_t i = 0; i < colvars.size(); i++) { cvm::real const *f = &(hills_energy_gradients->value (curr_bin)); colvar_forces[i].real_value += -1.0 * f[i]; // the gradients // are stored, not // the forces } } else { // we're off the grid, computing analytically only the hills // within range calc_hills (hills_off_grid.begin(), hills_off_grid.end(), colvar_energy); for (size_t i = 0; i < colvars.size(); i++) { calc_hills_force (i, hills_off_grid.begin(), hills_off_grid.end(), colvar_forces); } } } else { // calculate the current value of each hill and add it to colvar_energy calc_hills (hills.begin(), hills.end(), colvar_energy); // calculate the current derivatives of each hill and add them to // colvar_forces for (size_t i = 0; i < colvars.size(); i++) { calc_hills_force (i, hills.begin(), hills.end(), colvar_forces); } } if (cvm::debug()) cvm::log ("Hills energy = "+cvm::to_str (colvar_energy)+ ", hills forces = "+cvm::to_str (colvar_forces)+".\n"); }

void colvarbias_meta::update_replica_files_registry (   )  [protected, virtual]

Read the names all replica output files which have been added, skipping the one which is currently being written to (called only when != ). Definition at line 648 of file colvarbias_meta.C. References colvarmodule::debug(), colvarmodule::fatal_error(), colvarmodule::log(), replica_files, replica_files_pos, and replica_files_registry. Referenced by read_restart(), and update(). { if (cvm::debug()) cvm::log ("Updating the list of replica files, currently containing "+ cvm::to_str (replica_files.size())+" elements.\n"); // update the list of replica files by reading those created after restarting std::ifstream reg_is (replica_files_registry.c_str()); if (reg_is.good()) { std::string s (""); while ((reg_is >> s) && s.size()) { if (s == replica_out_file_name) { // this is the file from this same job, skip it if (cvm::debug()) cvm::log ("Skipping this job's replica file, \""+s+"\".\n"); s = ""; continue; } bool already_loaded = false; std::list<std::string>::iterator rsi = replica_files.begin(); for ( ; rsi != replica_files.end(); rsi++) { if (s == *rsi) { // this file was already added to the list if (cvm::debug()) cvm::log ("Skipping a replica file already loaded, \""+(*rsi)+"\".\n"); already_loaded = true;; } } if ( (replica_files.size() == 0) || (!already_loaded) ) { // add this file to the registry if (cvm::debug()) cvm::log ("New replica file found: \""+s+"\".\n"); replica_files.push_back (s); replica_files_pos.push_back (0); } } s = ""; } else { cvm::fatal_error ("Error: cannot read the replica files registry, \""+ replica_files_registry+"\".\n"); } reg_is.close(); if (cvm::debug()) cvm::log ("The list of replica files now contains "+ cvm::to_str (replica_files.size())+" elements.\n"); }

std::ostream & colvarbias_meta::write_restart (  std::ostream &  os  )  [virtual]

Write the bias configuration to a restart file. Implements colvarbias. Definition at line 973 of file colvarbias_meta.C. References colvar_grid< T >::add_constant(), comm, dump_fes_save, hills, hills_energy, hills_energy_gradients, hills_off_grid, colvarmodule::log(), colvar_grid_scalar::maximum_value(), colvar_grid< T >::multiply_constant(), replica, replica_out_file_name, colvar_grid< T >::write_multicol(), colvar_grid_gradient::write_restart(), and colvar_grid_scalar::write_restart(). { os << "metadynamics {\n" << " configuration {\n" // << " id " << this->id << "\n" << " name " << this->name << "\n"; if (this->comm != single_replica) os << " replica " << this->replica << "\n"; os << " }\n"; if (this->comm == single_replica) { if (use_grids) { os << " hills_energy\n"; hills_energy->write_restart (os); os << " hills_energy_gradients\n"; hills_energy_gradients->write_restart (os); if (dump_fes) { cvm::real const max = hills_energy->maximum_value(); hills_energy->add_constant (-1.0 * max); hills_energy->multiply_constant (-1.0); // if this is the only free energy integrator, the pmf file // name is general, otherwise there is a label with the bias // name std::string const fes_file_name = ((cvm::n_meta_biases == 1) && (cvm::n_abf_biases == 0)) ? std::string (cvm::output_prefix+ (dump_fes_save ? "."+cvm::to_str (cvm::step_absolute()) : "")+ ".pmf") : std::string (cvm::output_prefix+"."+this->name+ (dump_fes_save ? "."+cvm::to_str (cvm::step_absolute()) : "")+ ".pmf"); std::ofstream fes_os (fes_file_name.c_str()); hills_energy->write_multicol (fes_os); // restore the grid to original values hills_energy->multiply_constant (-1.0); hills_energy->add_constant (max); } } if ( (!use_grids) || keep_hills ) { // write all the hills in memory for (std::list<hill>::const_iterator h = this->hills.begin(); h != this->hills.end(); h++) { os << *h; } } else { // write just those that need to be computed analytically for (std::list<hill>::const_iterator h = this->hills_off_grid.begin(); h != this->hills_off_grid.end(); h++) { os << *h; } } } else { cvm::log ("Hills from the metadynamics bias \""+ this->name+"\" have been previously saved in the file \""+ replica_out_file_name+"\".\n"); } os << "}\n\n"; return os; }

---

Member Data Documentation

bool colvarbias_meta::b_hills_traj [protected]

Write the hill logfile. Definition at line 148 of file colvarbias_meta.h. Referenced by colvarbias_meta().

colvar_grid_count* colvarbias_meta::boltzmann_counts [protected]

Boltzmann populations (integer version). Definition at line 240 of file colvarbias_meta.h.

std::string colvarbias_meta::boltzmann_counts_file [protected]

Boltzmann counts output file. These are discretized Boltzmann weights, useful e.g. to initialize the samples of an ABF calculation. boltzmann_weights_scale must be much larger than 1 for a proper discretization Definition at line 220 of file colvarbias_meta.h.

colvar_grid_scalar* colvarbias_meta::boltzmann_weights [protected]

Boltzmann populations (real version). Definition at line 237 of file colvarbias_meta.h.

std::string colvarbias_meta::boltzmann_weights_file [protected]

Boltzmann weights output file. Definition at line 212 of file colvarbias_meta.h.

cvm::real colvarbias_meta::boltzmann_weights_scale [protected]

Multiply the exponential weights by this constant. Definition at line 225 of file colvarbias_meta.h.

cvm::real colvarbias_meta::boltzmann_weights_temp [protected]

Temperature (in K) for Boltzmann weights. Definition at line 228 of file colvarbias_meta.h.

Communication colvarbias_meta::comm

Communication between different replicas. Definition at line 26 of file colvarbias_meta.h. Referenced by colvarbias_meta(), create_hill(), read_hill(), read_restart(), update(), and write_restart().

bool colvarbias_meta::dump_fes [protected]

Dump the free energy surface (.pmf file) every restartFrequency. Definition at line 119 of file colvarbias_meta.h. Referenced by colvarbias_meta().

bool colvarbias_meta::dump_fes_save [protected]

Keep the free energy surface files at different iterations, appending a step number to each. Definition at line 123 of file colvarbias_meta.h. Referenced by colvarbias_meta(), and write_restart().

bool colvarbias_meta::expand_grids [protected]

Should the grids be expanded if necessary? Definition at line 109 of file colvarbias_meta.h. Referenced by colvarbias_meta().

colvar_grid_scalar* colvarbias_meta::free_energy [protected]

Free energy values. Definition at line 231 of file colvarbias_meta.h.

size_t colvarbias_meta::free_energy_begin [protected]

Select only hills after this step. Definition at line 194 of file colvarbias_meta.h.

size_t colvarbias_meta::free_energy_end [protected]

Select only hills before this step. Definition at line 197 of file colvarbias_meta.h.

std::string colvarbias_meta::free_energy_file [protected]

Free energy surface output file. Definition at line 206 of file colvarbias_meta.h.

colvar_grid_gradient* colvarbias_meta::free_energy_gradients [protected]

Free energy gradients. Definition at line 234 of file colvarbias_meta.h.

std::string colvarbias_meta::free_energy_gradients_file [protected]

Free energy gradients output file. Definition at line 209 of file colvarbias_meta.h.

cvm::real colvarbias_meta::free_energy_offset [protected]

Subtract this value from the free energy (after. Definition at line 203 of file colvarbias_meta.h.

size_t colvarbias_meta::grids_freq [protected]

How often the hills should be projected onto the grids. Definition at line 112 of file colvarbias_meta.h. Referenced by colvarbias_meta().

cvm::real colvarbias_meta::hill_weight [protected]

Height of new hills. Definition at line 99 of file colvarbias_meta.h. Referenced by colvarbias_meta(), read_hill(), and update().

cvm::real colvarbias_meta::hill_width [protected]

width of a hill The local width of each collective variable, multiplied by this number, provides the hill width along that direction Definition at line 142 of file colvarbias_meta.h. Referenced by colvarbias_meta(), and update().

std::list<hill> colvarbias_meta::hills [protected]

Parse analysis tasks and options List of hills used on this bias (total); if a grid is employed, these don't need to be updated at every time step. Definition at line 53 of file colvarbias_meta.h. Referenced by create_hill(), project_hills(), read_hill(), read_replica_files(), read_restart(), update(), and write_restart().

colvar_grid_scalar* colvarbias_meta::hills_energy [protected]

Hill energy, cached on a grid. Definition at line 126 of file colvarbias_meta.h. Referenced by colvarbias_meta(), create_hill(), project_hills(), read_hill(), read_restart(), recount_hills_off_grid(), update(), write_restart(), and ~colvarbias_meta().

colvar_grid_gradient* colvarbias_meta::hills_energy_gradients [protected]

Hill forces, cached on a grid. Definition at line 129 of file colvarbias_meta.h. Referenced by colvarbias_meta(), read_restart(), update(), write_restart(), and ~colvarbias_meta().

std::list<hill> colvarbias_meta::hills_off_grid [protected]

List of hills used on this bias that are on the boundary edges; these are updated regardless of whether hills are used. Definition at line 61 of file colvarbias_meta.h. Referenced by create_hill(), read_hill(), recount_hills_off_grid(), update(), and write_restart().

std::ofstream colvarbias_meta::hills_traj_os [protected]

Logfile of hill management (creation and deletion). Definition at line 150 of file colvarbias_meta.h. Referenced by colvarbias_meta(), create_hill(), read_replica_files(), and ~colvarbias_meta().

bool colvarbias_meta::keep_hills [protected]

Whether to keep the hills in the restart file (e.g. to do meaningful accurate rebinning afterwards). Definition at line 116 of file colvarbias_meta.h. Referenced by colvarbias_meta(), and read_restart().

size_t colvarbias_meta::new_hill_freq [protected]

Number of simulation steps between two hills. Definition at line 145 of file colvarbias_meta.h. Referenced by colvarbias_meta().

hill_iter colvarbias_meta::new_hills_begin [protected]

Iterator to the first of the "newest" hills (when using grids, those who haven't been mapped yet). Definition at line 57 of file colvarbias_meta.h. Referenced by create_hill(), read_hill(), read_restart(), and update().

hill_iter colvarbias_meta::new_hills_off_grid_begin [protected]

Same as new_hills_begin, but for the off-grid ones. Definition at line 64 of file colvarbias_meta.h.

bool colvarbias_meta::rebin_grids [protected]

Rebin the hills upon restarting. Definition at line 106 of file colvarbias_meta.h. Referenced by colvarbias_meta().

std::string colvarbias_meta::replica [protected]

Identifier for this replica. Definition at line 154 of file colvarbias_meta.h. Referenced by colvarbias_meta(), create_hill(), read_hill(), update(), and write_restart().

std::list<std::string> colvarbias_meta::replica_files [protected]

Replicas file names. Definition at line 179 of file colvarbias_meta.h. Referenced by read_replica_files(), and update_replica_files_registry().

std::list<size_t> colvarbias_meta::replica_files_pos [protected]

Positions in replica files (files are reopened at these positions). Definition at line 182 of file colvarbias_meta.h. Referenced by read_replica_files(), and update_replica_files_registry().

std::string colvarbias_meta::replica_files_registry [protected]

List of hill files from all the replicas. Definition at line 176 of file colvarbias_meta.h. Referenced by colvarbias_meta(), register_replica_file(), and update_replica_files_registry().

std::ofstream colvarbias_meta::replica_out_file [protected]

File to contain the hills created by this replica in this run. Definition at line 185 of file colvarbias_meta.h. Referenced by colvarbias_meta(), create_hill(), update(), and ~colvarbias_meta().

std::string colvarbias_meta::replica_out_file_name [protected]

File to contain the hills created by this replica in this run (name). Definition at line 188 of file colvarbias_meta.h. Referenced by colvarbias_meta(), and write_restart().

size_t colvarbias_meta::replica_update_freq [protected]

Frequency at which output files from other replicas are checked. Definition at line 173 of file colvarbias_meta.h. Referenced by colvarbias_meta().

bool colvarbias_meta::shift_fes [protected]

Make the free energy surface be larger than or equal to zero. Definition at line 200 of file colvarbias_meta.h.

bool colvarbias_meta::use_grids [protected]

Bin the hills on grids of energy and forces, and use them to force the colvars (as opposed to deriving the hills analytically). Definition at line 103 of file colvarbias_meta.h. Referenced by colvarbias_meta().

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The documentation for this class was generated from the following files:

• colvarbias_meta.h
• colvarbias_meta.C

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