forked from lijiext/lammps
1710 lines
59 KiB
C++
1710 lines
59 KiB
C++
#include <iostream>
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#include <sstream>
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#include <fstream>
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#include <iomanip>
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#include <cmath>
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#include <algorithm>
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// used to set the absolute path of a replica file
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#if defined (WIN32) && !defined(__CYGWIN__)
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#include <direct.h>
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#define CHDIR ::_chdir
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#define GETCWD ::_getcwd
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#define PATHSEP "\\"
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#else
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#include <unistd.h>
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#define CHDIR ::chdir
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#define GETCWD ::getcwd
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#define PATHSEP "/"
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#endif
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#include "colvar.h"
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#include "colvarbias_meta.h"
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colvarbias_meta::colvarbias_meta()
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: colvarbias(),
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state_file_step (0),
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new_hills_begin (hills.end())
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{
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}
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colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
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: colvarbias (conf, key),
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state_file_step (0),
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new_hills_begin (hills.end())
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{
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if (cvm::n_abf_biases > 0)
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cvm::log ("Warning: ABF and metadynamics running at the "
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"same time can lead to inconsistent results.\n");
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get_keyval (conf, "hillWeight", hill_weight, 0.01);
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if (hill_weight == 0.0)
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cvm::log ("Warning: hillWeight has been set to zero, "
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"this bias will have no effect.\n");
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get_keyval (conf, "newHillFrequency", new_hill_freq, 1000);
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get_keyval (conf, "hillWidth", hill_width, std::sqrt (2.0 * PI) / 2.0);
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get_keyval (conf, "useGrids", use_grids, true);
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if (use_grids) {
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get_keyval (conf, "gridsUpdateFrequency", grids_freq, new_hill_freq);
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get_keyval (conf, "rebinGrids", rebin_grids, false);
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expand_grids = false;
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for (size_t i = 0; i < colvars.size(); i++) {
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if (colvars[i]->expand_boundaries) {
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expand_grids = true;
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cvm::log ("Metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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": Will expand grids when the colvar \""+
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colvars[i]->name+"\" approaches its boundaries.\n");
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}
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}
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get_keyval (conf, "keepHills", keep_hills, false);
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get_keyval (conf, "dumpFreeEnergyFile", dump_fes, true);
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get_keyval (conf, "saveFreeEnergyFile", dump_fes_save, false);
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for (size_t i = 0; i < colvars.size(); i++) {
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colvars[i]->enable (colvar::task_grid);
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}
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hills_energy = new colvar_grid_scalar (colvars);
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hills_energy_gradients = new colvar_grid_gradient (colvars);
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} else {
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rebin_grids = false;
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keep_hills = false;
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dump_fes = false;
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dump_fes_save = false;
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dump_replica_fes = false;
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}
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{
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bool b_replicas = false;
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get_keyval (conf, "multipleReplicas", b_replicas, false);
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if (b_replicas)
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comm = multiple_replicas;
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else
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comm = single_replica;
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}
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if (comm != single_replica) {
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if (expand_grids)
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cvm::fatal_error ("Error: expandBoundaries is not supported when "
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"using more than one replicas; please allocate "
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"wide enough boundaries for each colvar"
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"ahead of time.\n");
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if (get_keyval (conf, "dumpPartialFreeEnergyFile", dump_replica_fes, false)) {
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if (dump_replica_fes && (! dump_fes)) {
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cvm::log ("Enabling \"dumpFreeEnergyFile\".\n");
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}
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}
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get_keyval (conf, "replicaID", replica_id, std::string (""));
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if (!replica_id.size())
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cvm::fatal_error ("Error: replicaID must be defined "
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"when using more than one replica.\n");
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get_keyval (conf, "replicasRegistry",
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replicas_registry_file,
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(this->name+".replicas.registry.txt"));
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get_keyval (conf, "replicaUpdateFrequency",
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replica_update_freq, new_hill_freq);
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if (keep_hills)
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cvm::log ("Warning: in metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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": keepHills with more than one replica can lead to a very "
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"large amount input/output and slow down your calculations. "
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"Please consider disabling it.\n");
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{
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// TODO: one may want to specify the path manually for intricated filesystems?
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char *pwd = new char[3001];
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if (GETCWD (pwd, 3000) == NULL)
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cvm::fatal_error ("Error: cannot get the path of the current working directory.\n");
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replica_list_file =
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(std::string (pwd)+std::string (PATHSEP)+
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this->name+"."+replica_id+".files.txt");
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// replica_hills_file and replica_state_file are those written
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// by the current replica; within the mirror biases, they are
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// those by another replica
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replica_hills_file =
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(std::string (pwd)+std::string (PATHSEP)+
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cvm::output_prefix+".colvars."+this->name+"."+replica_id+".hills");
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replica_state_file =
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(std::string (pwd)+std::string (PATHSEP)+
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cvm::output_prefix+".colvars."+this->name+"."+replica_id+".state");
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delete pwd;
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}
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// now register this replica
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// first check that it isn't already there
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bool registered_replica = false;
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std::ifstream reg_is (replicas_registry_file.c_str());
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if (reg_is.good()) { // the file may not be there yet
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std::string existing_replica ("");
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std::string existing_replica_file ("");
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while ((reg_is >> existing_replica) && existing_replica.size() &&
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(reg_is >> existing_replica_file) && existing_replica_file.size()) {
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if (existing_replica == replica_id) {
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// this replica was already registered
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replica_list_file = existing_replica_file;
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reg_is.close();
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registered_replica = true;
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break;
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}
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}
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reg_is.close();
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}
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// if this replica was not included yet, we should generate a
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// new record for it: but first, we write this replica's files,
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// for the others to read
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// open the "hills" buffer file
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replica_hills_os.open (replica_hills_file.c_str());
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if (!replica_hills_os.good())
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cvm::fatal_error ("Error: in opening file \""+
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replica_hills_file+"\" for writing.\n");
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replica_hills_os.setf (std::ios::scientific, std::ios::floatfield);
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// write the state file (so that there is always one available)
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write_replica_state_file();
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// schedule to read the state files of the other replicas
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for (size_t ir = 0; ir < replicas.size(); ir++) {
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(replicas[ir])->replica_state_file_in_sync = false;
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}
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// if we're running without grids, use a growing list of "hills" files
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// otherwise, just one state file and one "hills" file as buffer
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std::ofstream list_os (replica_list_file.c_str(),
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(use_grids ? std::ios::trunc : std::ios::app));
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if (! list_os.good())
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cvm::fatal_error ("Error: in opening file \""+
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replica_list_file+"\" for writing.\n");
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list_os << "stateFile " << replica_state_file << "\n";
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list_os << "hillsFile " << replica_hills_file << "\n";
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list_os.close();
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// finally, if add a new record for this replica to the registry
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if (! registered_replica) {
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std::ofstream reg_os (replicas_registry_file.c_str(), std::ios::app);
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if (! reg_os.good())
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cvm::fatal_error ("Error: in opening file \""+
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replicas_registry_file+"\" for writing.\n");
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reg_os << replica_id << " " << replica_list_file << "\n";
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reg_os.close();
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}
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}
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get_keyval (conf, "writeHillsTrajectory", b_hills_traj, false);
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if (b_hills_traj) {
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std::string const traj_file_name (cvm::output_prefix+
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".colvars."+this->name+
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( (comm != single_replica) ?
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("."+replica_id) :
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("") )+
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".hills.traj");
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hills_traj_os.open (traj_file_name.c_str());
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if (!hills_traj_os.good())
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cvm::fatal_error ("Error: in opening hills output file \"" +
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traj_file_name + "\".\n");
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}
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// for well-tempered metadynamics
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get_keyval (conf, "wellTempered", well_tempered, false);
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get_keyval (conf, "biasTemperature", bias_temperature, -1.0);
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if ((bias_temperature == -1.0) && well_tempered) {
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cvm::fatal_error ("Error: biasTemperature is not set.\n");
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}
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if (well_tempered) {
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cvm::log("Well-tempered metadynamics is used.\n");
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cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n");
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}
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if (cvm::debug())
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cvm::log ("Done initializing the metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
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save_delimiters = false;
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}
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colvarbias_meta::~colvarbias_meta()
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{
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if (hills_energy) {
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delete hills_energy;
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hills_energy = NULL;
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}
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if (hills_energy_gradients) {
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delete hills_energy_gradients;
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hills_energy_gradients = NULL;
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}
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if (replica_hills_os.good())
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replica_hills_os.close();
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if (hills_traj_os.good())
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hills_traj_os.close();
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}
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// **********************************************************************
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// Hill management member functions
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// **********************************************************************
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std::list<colvarbias_meta::hill>::const_iterator
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colvarbias_meta::create_hill (colvarbias_meta::hill const &h)
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{
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hill_iter const hills_end = hills.end();
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hills.push_back (h);
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if (new_hills_begin == hills_end) {
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// if new_hills_begin is unset, set it for the first time
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new_hills_begin = hills.end();
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new_hills_begin--;
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}
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if (use_grids) {
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// also add it to the list of hills that are off-grid, which may
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// need to be computed analytically when the colvar returns
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// off-grid
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cvm::real const min_dist = hills_energy->bin_distance_from_boundaries (h.centers, true);
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if (min_dist < (3.0 * std::floor (hill_width)) + 1.0) {
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hills_off_grid.push_back (h);
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}
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}
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// output to trajectory (if specified)
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if (hills_traj_os.good()) {
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hills_traj_os << (hills.back()).output_traj();
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if (cvm::debug()) {
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hills_traj_os.flush();
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}
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}
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has_data = true;
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return hills.end();
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}
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std::list<colvarbias_meta::hill>::const_iterator
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colvarbias_meta::delete_hill (hill_iter &h)
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{
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if (cvm::debug()) {
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cvm::log ("Deleting hill from the metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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", with step number "+
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cvm::to_str (h->it)+(h->replica.size() ?
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", replica id \""+h->replica :
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"")+".\n");
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}
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if (use_grids && hills_off_grid.size()) {
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for (hill_iter hoff = hills_off_grid.begin();
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hoff != hills_off_grid.end(); hoff++) {
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if (*h == *hoff) {
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hills_off_grid.erase (hoff);
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break;
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}
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}
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}
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if (hills_traj_os.good()) {
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// output to the trajectory
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hills_traj_os << "# DELETED this hill: "
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<< (hills.back()).output_traj()
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<< "\n";
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if (cvm::debug())
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hills_traj_os.flush();
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}
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return hills.erase (h);
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}
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cvm::real colvarbias_meta::update()
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{
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if (cvm::debug())
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cvm::log ("Updating the metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
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if (use_grids) {
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std::vector<int> curr_bin = hills_energy->get_colvars_index();
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if (expand_grids) {
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// first of all, expand the grids, if specified
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if (cvm::debug())
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cvm::log ("Metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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": current coordinates on the grid: "+
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cvm::to_str (curr_bin)+".\n");
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bool changed_grids = false;
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int const min_buffer =
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(3 * (size_t) std::floor (hill_width)) + 1;
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std::vector<int> new_sizes (hills_energy->sizes());
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std::vector<colvarvalue> new_lower_boundaries (hills_energy->lower_boundaries);
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std::vector<colvarvalue> new_upper_boundaries (hills_energy->upper_boundaries);
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for (size_t i = 0; i < colvars.size(); i++) {
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if (! colvars[i]->expand_boundaries)
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continue;
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cvm::real &new_lb = new_lower_boundaries[i].real_value;
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cvm::real &new_ub = new_upper_boundaries[i].real_value;
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int &new_size = new_sizes[i];
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bool changed_lb = false, changed_ub = false;
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if (curr_bin[i] < min_buffer) {
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int const extra_points = (min_buffer - curr_bin[i]);
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new_lb -= extra_points * colvars[i]->width;
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new_size += extra_points;
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// changed offset in this direction => the pointer needs to
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// be changed, too
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curr_bin[i] += extra_points;
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changed_lb = true;
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cvm::log ("Metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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": new lower boundary for colvar \""+
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colvars[i]->name+"\", at "+
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cvm::to_str (new_lower_boundaries[i])+".\n");
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}
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if (curr_bin[i] > new_size - min_buffer - 1) {
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int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer);
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new_ub += extra_points * colvars[i]->width;
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new_size += extra_points;
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changed_ub = true;
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cvm::log ("Metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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": new upper boundary for colvar \""+
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colvars[i]->name+"\", at "+
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cvm::to_str (new_upper_boundaries[i])+".\n");
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}
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if (changed_lb || changed_ub)
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changed_grids = true;
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}
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if (changed_grids) {
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// map everything into new grids
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colvar_grid_scalar *new_hills_energy =
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new colvar_grid_scalar (*hills_energy);
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colvar_grid_gradient *new_hills_energy_gradients =
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new colvar_grid_gradient (*hills_energy_gradients);
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// supply new boundaries to the new grids
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new_hills_energy->lower_boundaries = new_lower_boundaries;
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new_hills_energy->upper_boundaries = new_upper_boundaries;
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new_hills_energy->create (new_sizes, 0.0, 1);
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new_hills_energy_gradients->lower_boundaries = new_lower_boundaries;
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new_hills_energy_gradients->upper_boundaries = new_upper_boundaries;
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new_hills_energy_gradients->create (new_sizes, 0.0, colvars.size());
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new_hills_energy->map_grid (*hills_energy);
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new_hills_energy_gradients->map_grid (*hills_energy_gradients);
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delete hills_energy;
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delete hills_energy_gradients;
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hills_energy = new_hills_energy;
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hills_energy_gradients = new_hills_energy_gradients;
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curr_bin = hills_energy->get_colvars_index();
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if (cvm::debug())
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cvm::log ("Coordinates on the new grid: "+
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cvm::to_str (curr_bin)+".\n");
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}
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}
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}
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// add a new hill if the required time interval has passed
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if ((cvm::step_absolute() % new_hill_freq) == 0) {
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if (cvm::debug())
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cvm::log ("Metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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": adding a new hill at step "+cvm::to_str (cvm::step_absolute())+".\n");
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switch (comm) {
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case single_replica:
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if (well_tempered) {
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std::vector<int> curr_bin = hills_energy->get_colvars_index();
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cvm::real const hills_energy_sum_here = hills_energy->value(curr_bin);
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cvm::real const exp_weight = std::exp(-hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
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create_hill (hill ((hill_weight*exp_weight), colvars, hill_width));
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} else {
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create_hill (hill (hill_weight, colvars, hill_width));
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}
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break;
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case multiple_replicas:
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if (well_tempered) {
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std::vector<int> curr_bin = hills_energy->get_colvars_index();
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cvm::real const hills_energy_sum_here = hills_energy->value(curr_bin);
|
|
cvm::real const exp_weight = std::exp(-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));
|
|
}
|
|
if (replica_hills_os.good()) {
|
|
replica_hills_os << hills.back();
|
|
} else {
|
|
cvm::fatal_error ("Error: in metadynamics bias \""+this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
" while writing hills for the other replicas.\n");
|
|
}
|
|
break;
|
|
}
|
|
}
|
|
|
|
// sync with the other replicas (if needed)
|
|
if (comm != single_replica) {
|
|
|
|
// reread the replicas registry
|
|
if ((cvm::step_absolute() % replica_update_freq) == 0) {
|
|
update_replicas_registry();
|
|
// empty the output buffer
|
|
replica_hills_os.flush();
|
|
|
|
read_replica_files();
|
|
}
|
|
}
|
|
|
|
// calculate the biasing energy and forces
|
|
bias_energy = 0.0;
|
|
for (size_t ir = 0; ir < colvars.size(); ir++) {
|
|
colvar_forces[ir].reset();
|
|
}
|
|
if (comm == multiple_replicas)
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
replicas[ir]->bias_energy = 0.0;
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
replicas[ir]->colvar_forces[ic].reset();
|
|
}
|
|
}
|
|
|
|
if (use_grids) {
|
|
|
|
// get the forces from the grid
|
|
|
|
if ((cvm::step_absolute() % 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();
|
|
|
|
// TODO: we may want to condense all into one replicas array,
|
|
// including "this" as the first element
|
|
if (comm == multiple_replicas) {
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
replicas[ir]->project_hills (replicas[ir]->new_hills_begin,
|
|
replicas[ir]->hills.end(),
|
|
replicas[ir]->hills_energy,
|
|
replicas[ir]->hills_energy_gradients);
|
|
replicas[ir]->new_hills_begin = replicas[ir]->hills.end();
|
|
}
|
|
}
|
|
}
|
|
|
|
std::vector<int> curr_bin = hills_energy->get_colvars_index();
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
": 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
|
|
|
|
bias_energy += hills_energy->value (curr_bin);
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
cvm::real const *f = &(hills_energy_gradients->value (curr_bin));
|
|
colvar_forces[ic].real_value += -1.0 * f[ic];
|
|
// the gradients are stored, not the forces
|
|
}
|
|
if (comm == multiple_replicas)
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
bias_energy += replicas[ir]->hills_energy->value (curr_bin);
|
|
cvm::real const *f = &(replicas[ir]->hills_energy_gradients->value (curr_bin));
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
colvar_forces[ic].real_value += -1.0 * f[ic];
|
|
}
|
|
}
|
|
|
|
} else {
|
|
|
|
// off the grid: compute analytically only the hills at the grid's edges
|
|
|
|
calc_hills (hills_off_grid.begin(), hills_off_grid.end(), bias_energy);
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
calc_hills_force (ic, hills_off_grid.begin(), hills_off_grid.end(), colvar_forces);
|
|
}
|
|
|
|
if (comm == multiple_replicas)
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
calc_hills (replicas[ir]->hills_off_grid.begin(),
|
|
replicas[ir]->hills_off_grid.end(),
|
|
bias_energy);
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
calc_hills_force (ic,
|
|
replicas[ir]->hills_off_grid.begin(),
|
|
replicas[ir]->hills_off_grid.end(),
|
|
colvar_forces);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
// now include the hills that have not been binned yet (starting
|
|
// from new_hills_begin)
|
|
|
|
calc_hills (new_hills_begin, hills.end(), bias_energy);
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
calc_hills_force (ic, new_hills_begin, hills.end(), colvar_forces);
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Hills energy = "+cvm::to_str (bias_energy)+
|
|
", hills forces = "+cvm::to_str (colvar_forces)+".\n");
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
": adding the forces from the other replicas.\n");
|
|
|
|
if (comm == multiple_replicas)
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
calc_hills (replicas[ir]->new_hills_begin,
|
|
replicas[ir]->hills.end(),
|
|
bias_energy);
|
|
for (size_t ic = 0; ic < colvars.size(); ic++) {
|
|
calc_hills_force (ic,
|
|
replicas[ir]->new_hills_begin,
|
|
replicas[ir]->hills.end(),
|
|
colvar_forces);
|
|
}
|
|
if (cvm::debug())
|
|
cvm::log ("Hills energy = "+cvm::to_str (bias_energy)+
|
|
", hills forces = "+cvm::to_str (colvar_forces)+".\n");
|
|
}
|
|
|
|
return bias_energy;
|
|
}
|
|
|
|
|
|
void colvarbias_meta::calc_hills (colvarbias_meta::hill_iter h_first,
|
|
colvarbias_meta::hill_iter h_last,
|
|
cvm::real &energy,
|
|
std::vector<colvarvalue> const &colvar_values)
|
|
{
|
|
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 ¢er = 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 (std::exp (-0.5*cv_sqdev));
|
|
}
|
|
energy += h->energy();
|
|
}
|
|
}
|
|
|
|
|
|
void colvarbias_meta::calc_hills_force (size_t const &i,
|
|
colvarbias_meta::hill_iter h_first,
|
|
colvarbias_meta::hill_iter h_last,
|
|
std::vector<colvarvalue> &forces,
|
|
std::vector<colvarvalue> const &values)
|
|
{
|
|
// 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 ¢er = 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 ¢er = 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 ¢er = 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;
|
|
}
|
|
}
|
|
|
|
|
|
// **********************************************************************
|
|
// grid management functions
|
|
// **********************************************************************
|
|
|
|
void colvarbias_meta::project_hills (colvarbias_meta::hill_iter h_first,
|
|
colvarbias_meta::hill_iter h_last,
|
|
colvar_grid_scalar *he,
|
|
colvar_grid_gradient *hg,
|
|
bool print_progress)
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
": projecting hills.\n");
|
|
|
|
// TODO: improve it by looping over a small subgrid instead of the whole grid
|
|
|
|
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);
|
|
|
|
size_t count = 0;
|
|
size_t const print_frequency = ((hills.size() >= 1000000) ? 1 : (1000000/(hills.size()+1)));
|
|
|
|
if (hg != NULL) {
|
|
|
|
// loop over the points of the grid
|
|
for ( ;
|
|
(he->index_ok (he_ix)) && (hg->index_ok (hg_ix));
|
|
count++) {
|
|
|
|
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, hills_energy_here);
|
|
|
|
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] = hills_forces_here[i].real_value;
|
|
}
|
|
hg->acc_force (hg_ix, &(colvar_forces_scalar.front()));
|
|
|
|
he->incr (he_ix);
|
|
hg->incr (hg_ix);
|
|
|
|
if ((count % print_frequency) == 0) {
|
|
if (print_progress) {
|
|
cvm::real const progress = cvm::real (count) / cvm::real (hg->number_of_points());
|
|
std::ostringstream os;
|
|
os.setf (std::ios::fixed, std::ios::floatfield);
|
|
os << std::setw (6) << std::setprecision (2)
|
|
<< 100.0 * progress
|
|
<< "% done.";
|
|
cvm::log (os.str());
|
|
}
|
|
}
|
|
}
|
|
|
|
} else {
|
|
|
|
// simpler version, with just the energy
|
|
|
|
for ( ; (he->index_ok (he_ix)); ) {
|
|
|
|
for (size_t i = 0; i < colvars.size(); i++) {
|
|
colvar_values[i] = hills_energy->bin_to_value_scalar (he_ix[i], i);
|
|
}
|
|
|
|
hills_energy_here = 0.0;
|
|
calc_hills (h_first, h_last, hills_energy_here, colvar_values);
|
|
he->acc_value (he_ix, hills_energy_here);
|
|
|
|
he->incr (he_ix);
|
|
|
|
count++;
|
|
if ((count % print_frequency) == 0) {
|
|
if (print_progress) {
|
|
cvm::real const progress = cvm::real (count) / cvm::real (he->number_of_points());
|
|
std::ostringstream os;
|
|
os.setf (std::ios::fixed, std::ios::floatfield);
|
|
os << std::setw (6) << std::setprecision (2)
|
|
<< 100.0 * progress
|
|
<< "% done.";
|
|
cvm::log (os.str());
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
if (print_progress) {
|
|
cvm::log ("100.00% done.");
|
|
}
|
|
|
|
if (! keep_hills) {
|
|
hills.erase (hills.begin(), hills.end());
|
|
}
|
|
}
|
|
|
|
|
|
void colvarbias_meta::recount_hills_off_grid (colvarbias_meta::hill_iter h_first,
|
|
colvarbias_meta::hill_iter h_last,
|
|
colvar_grid_scalar *he)
|
|
{
|
|
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, true);
|
|
if (min_dist < (3.0 * std::floor (hill_width)) + 1.0) {
|
|
hills_off_grid.push_back (*h);
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
|
|
// **********************************************************************
|
|
// multiple replicas functions
|
|
// **********************************************************************
|
|
|
|
|
|
void colvarbias_meta::update_replicas_registry()
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": updating the list of replicas, currently containing "+
|
|
cvm::to_str (replicas.size())+" elements.\n");
|
|
|
|
{
|
|
// copy the whole file into a string for convenience
|
|
std::string line ("");
|
|
std::ifstream reg_file (replicas_registry_file.c_str());
|
|
if (reg_file.good()) {
|
|
replicas_registry.clear();
|
|
while (colvarparse::getline_nocomments (reg_file, line))
|
|
replicas_registry.append (line+"\n");
|
|
} else {
|
|
cvm::fatal_error ("Error: failed to open file \""+replicas_registry_file+
|
|
"\" for reading.\n");
|
|
}
|
|
}
|
|
|
|
// now parse it
|
|
std::istringstream reg_is (replicas_registry);
|
|
if (reg_is.good()) {
|
|
|
|
std::string new_replica ("");
|
|
std::string new_replica_file ("");
|
|
while ((reg_is >> new_replica) && new_replica.size() &&
|
|
(reg_is >> new_replica_file) && new_replica_file.size()) {
|
|
|
|
if (new_replica == this->replica_id) {
|
|
// this is the record for this same replica, skip it
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
": skipping this replica's own record: \""+
|
|
new_replica+"\", \""+new_replica_file+"\"\n");
|
|
new_replica_file.clear();
|
|
new_replica.clear();
|
|
continue;
|
|
}
|
|
|
|
bool already_loaded = false;
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
if (new_replica == (replicas[ir])->replica_id) {
|
|
// this replica was already added
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
": skipping a replica already loaded, \""+
|
|
(replicas[ir])->replica_id+"\".\n");
|
|
already_loaded = true;
|
|
break;
|
|
}
|
|
}
|
|
|
|
if (!already_loaded) {
|
|
// add this replica to the registry
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": accessing replica \""+new_replica+"\".\n");
|
|
replicas.push_back (new colvarbias_meta());
|
|
(replicas.back())->replica_id = new_replica;
|
|
(replicas.back())->replica_list_file = new_replica_file;
|
|
(replicas.back())->replica_state_file = "";
|
|
(replicas.back())->replica_state_file_in_sync = false;
|
|
|
|
// Note: the following could become a copy constructor?
|
|
(replicas.back())->name = this->name;
|
|
(replicas.back())->colvars = colvars;
|
|
(replicas.back())->use_grids = use_grids;
|
|
(replicas.back())->dump_fes = false;
|
|
(replicas.back())->expand_grids = false;
|
|
(replicas.back())->rebin_grids = false;
|
|
(replicas.back())->keep_hills = false;
|
|
(replicas.back())->colvar_forces = colvar_forces;
|
|
|
|
(replicas.back())->comm = multiple_replicas;
|
|
|
|
if (use_grids) {
|
|
(replicas.back())->hills_energy = new colvar_grid_scalar (colvars);
|
|
(replicas.back())->hills_energy_gradients = new colvar_grid_gradient (colvars);
|
|
}
|
|
}
|
|
}
|
|
|
|
// continue the cycle
|
|
new_replica_file = "";
|
|
new_replica = "";
|
|
} else {
|
|
cvm::fatal_error ("Error: cannot read the replicas registry file \""+
|
|
replicas_registry+"\".\n");
|
|
}
|
|
|
|
// now (re)read the list file of each replica
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": reading the list file for replica \""+
|
|
(replicas[ir])->replica_id+"\".\n");
|
|
|
|
std::ifstream list_is ((replicas[ir])->replica_list_file.c_str());
|
|
std::string key;
|
|
std::string new_state_file, new_hills_file;
|
|
if (!(list_is >> key) ||
|
|
!(key == std::string ("stateFile")) ||
|
|
!(list_is >> new_state_file) ||
|
|
!(list_is >> key) ||
|
|
!(key == std::string ("hillsFile")) ||
|
|
!(list_is >> new_hills_file)) {
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": failed to read the file \""+
|
|
(replicas[ir])->replica_list_file+"\": will try again after "+
|
|
cvm::to_str (replica_update_freq)+" steps.\n");
|
|
(replicas[ir])->update_status++;
|
|
} else {
|
|
(replicas[ir])->update_status = 0;
|
|
if (new_state_file != (replicas[ir])->replica_state_file) {
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": replica \""+(replicas[ir])->replica_id+
|
|
"\" has supplied a new state file, \""+new_state_file+
|
|
"\".\n");
|
|
(replicas[ir])->replica_state_file_in_sync = false;
|
|
(replicas[ir])->replica_state_file = new_state_file;
|
|
(replicas[ir])->replica_hills_file = new_hills_file;
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\": the list of replicas contains "+
|
|
cvm::to_str (replicas.size())+" elements.\n");
|
|
}
|
|
|
|
|
|
void colvarbias_meta::read_replica_files()
|
|
{
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
|
|
if (! (replicas[ir])->replica_state_file_in_sync) {
|
|
// if a new state file is being read, the hills file is also new
|
|
(replicas[ir])->replica_hills_file_pos = 0;
|
|
}
|
|
|
|
// (re)read the state file if necessary
|
|
if ( (! (replicas[ir])->has_data) ||
|
|
(! (replicas[ir])->replica_state_file_in_sync) ) {
|
|
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": reading the state of replica \""+
|
|
(replicas[ir])->replica_id+"\" from file \""+
|
|
(replicas[ir])->replica_state_file+"\".\n");
|
|
|
|
std::ifstream is ((replicas[ir])->replica_state_file.c_str());
|
|
if (! (replicas[ir])->read_restart (is)) {
|
|
cvm::log ("Reading from file \""+(replicas[ir])->replica_state_file+
|
|
"\" failed or incomplete: will try again in "+
|
|
cvm::to_str (replica_update_freq)+" steps.\n");
|
|
} else {
|
|
// state file has been read successfully
|
|
(replicas[ir])->replica_state_file_in_sync = true;
|
|
(replicas[ir])->update_status = 0;
|
|
}
|
|
is.close();
|
|
}
|
|
|
|
// now read the hills added after writing the state file
|
|
if ((replicas[ir])->replica_hills_file.size()) {
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": checking for new hills from replica \""+
|
|
(replicas[ir])->replica_id+"\" in the file \""+
|
|
(replicas[ir])->replica_hills_file+"\".\n");
|
|
|
|
// read hills from the other replicas' files; for each file, resume
|
|
// the position recorded previously
|
|
|
|
std::ifstream is ((replicas[ir])->replica_hills_file.c_str());
|
|
if (is.good()) {
|
|
|
|
// try to resume the previous position
|
|
is.seekg ((replicas[ir])->replica_hills_file_pos, std::ios::beg);
|
|
if (!is.good()){
|
|
// if fail (the file may have been overwritten), reset this
|
|
// position
|
|
is.clear();
|
|
is.seekg (0, std::ios::beg);
|
|
// reset the counter
|
|
(replicas[ir])->replica_hills_file_pos = 0;
|
|
// schedule to reread the state file
|
|
(replicas[ir])->replica_state_file_in_sync = false;
|
|
// and record the failure
|
|
(replicas[ir])->update_status++;
|
|
cvm::log ("Failed to read the file \""+(replicas[ir])->replica_hills_file+
|
|
"\" at the previous position: will try again in "+
|
|
cvm::to_str (replica_update_freq)+" steps.\n");
|
|
} else {
|
|
|
|
while ((replicas[ir])->read_hill (is)) {
|
|
// if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": received a hill from replica \""+
|
|
(replicas[ir])->replica_id+
|
|
"\" at step "+
|
|
cvm::to_str (((replicas[ir])->hills.back()).it)+".\n");
|
|
}
|
|
is.clear();
|
|
// store the position for the next read
|
|
(replicas[ir])->replica_hills_file_pos = is.tellg();
|
|
if (cvm::debug())
|
|
cvm::log ("Metadynamics bias \""+this->name+"\""+
|
|
": stopped reading file \""+(replicas[ir])->replica_hills_file+
|
|
"\" at position "+
|
|
cvm::to_str ((replicas[ir])->replica_hills_file_pos)+".\n");
|
|
|
|
// test whether this is the end of the file
|
|
is.seekg (0, std::ios::end);
|
|
if (is.tellg() > (replicas[ir])->replica_hills_file_pos+1) {
|
|
(replicas[ir])->update_status++;
|
|
} else {
|
|
(replicas[ir])->update_status = 0;
|
|
}
|
|
}
|
|
|
|
} else {
|
|
cvm::log ("Failed to read the file \""+(replicas[ir])->replica_hills_file+
|
|
"\": will try again in "+
|
|
cvm::to_str (replica_update_freq)+" steps.\n");
|
|
(replicas[ir])->update_status++;
|
|
// cvm::fatal_error ("Error: cannot read from file \""+
|
|
// (replicas[ir])->replica_hills_file+"\".\n");
|
|
}
|
|
is.close();
|
|
}
|
|
|
|
size_t const n_flush = (replica_update_freq/new_hill_freq + 1);
|
|
if ((replicas[ir])->update_status > 3*n_flush) {
|
|
// TODO: suspend the calculation?
|
|
cvm::log ("WARNING: in metadynamics bias \""+this->name+"\""+
|
|
" failed to read completely the output of replica \""+
|
|
(replicas[ir])->replica_id+
|
|
"\" after more than "+
|
|
cvm::to_str ((replicas[ir])->update_status * replica_update_freq)+
|
|
" steps. Ensure that it is still running.\n");
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
// **********************************************************************
|
|
// input functions
|
|
// **********************************************************************
|
|
|
|
|
|
std::istream & colvarbias_meta::read_restart (std::istream& is)
|
|
{
|
|
size_t const start_pos = is.tellg();
|
|
|
|
if (comm == single_replica) {
|
|
// if using a multiple replicas scheme, output messages
|
|
// are printed before and after calling this function
|
|
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)) ) {
|
|
|
|
if (comm == single_replica)
|
|
cvm::log ("Error: in reading restart configuration for metadynamics bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
(replica_state_file_in_sync ? ("at position "+
|
|
cvm::to_str (start_pos)+
|
|
" in the state file") : "")+".\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 different name: different system?\n");
|
|
|
|
if (name.size() == 0) {
|
|
cvm::fatal_error ("Error: \"metadynamics\" block within the restart file "
|
|
"has no identifiers.\n");
|
|
}
|
|
|
|
if (comm != single_replica) {
|
|
std::string replica = "";
|
|
if (colvarparse::get_keyval (conf, "replicaID", replica,
|
|
std::string (""), colvarparse::parse_silent) &&
|
|
(replica != this->replica_id))
|
|
cvm::fatal_error ("Error: in the restart file, the "
|
|
"\"metadynamics\" block has a different replicaID: different system?\n");
|
|
|
|
colvarparse::get_keyval (conf, "step", state_file_step,
|
|
cvm::step_absolute(), colvarparse::parse_silent);
|
|
}
|
|
|
|
bool grids_from_restart_file = use_grids;
|
|
|
|
if (use_grids) {
|
|
|
|
if (expand_grids) {
|
|
// the boundaries of the colvars may have been changed; TODO:
|
|
// this reallocation is only for backward-compatibility, and may
|
|
// be deleted when grid_parameters (i.e. colvargrid's own
|
|
// internal reallocation) 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);
|
|
}
|
|
|
|
colvar_grid_scalar *hills_energy_backup = NULL;
|
|
colvar_grid_gradient *hills_energy_gradients_backup = NULL;
|
|
|
|
if (has_data) {
|
|
if (cvm::debug())
|
|
cvm::log ("Backupping grids for metadynamics bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
|
|
hills_energy_backup = hills_energy;
|
|
hills_energy_gradients_backup = hills_energy_gradients;
|
|
hills_energy = new colvar_grid_scalar (colvars);
|
|
hills_energy_gradients = new colvar_grid_gradient (colvars);
|
|
}
|
|
|
|
size_t const hills_energy_pos = is.tellg();
|
|
if (!(is >> key)) {
|
|
if (hills_energy_backup != NULL) {
|
|
delete hills_energy;
|
|
delete hills_energy_gradients;
|
|
hills_energy = hills_energy_backup;
|
|
hills_energy_gradients = hills_energy_gradients_backup;
|
|
}
|
|
is.clear();
|
|
is.seekg (hills_energy_pos, std::ios::beg);
|
|
is.setstate (std::ios::failbit);
|
|
return is;
|
|
} else if (!(key == std::string ("hills_energy")) ||
|
|
!(hills_energy->read_restart (is))) {
|
|
is.clear();
|
|
is.seekg (hills_energy_pos, std::ios::beg);
|
|
grids_from_restart_file = false;
|
|
if (!rebin_grids) {
|
|
if (hills_energy_backup == NULL)
|
|
cvm::fatal_error ("Error: couldn't read the free energy grid for metadynamics bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
"; if useGrids was off when the state file was written, "
|
|
"enable rebinGrids now to regenerate the grids.\n");
|
|
else {
|
|
if (comm == single_replica)
|
|
cvm::log ("Error: couldn't read the free energy grid for metadynamics bias \""+
|
|
this->name+"\".\n");
|
|
delete hills_energy;
|
|
delete hills_energy_gradients;
|
|
hills_energy = hills_energy_backup;
|
|
hills_energy_gradients = hills_energy_gradients_backup;
|
|
is.setstate (std::ios::failbit);
|
|
return is;
|
|
}
|
|
}
|
|
}
|
|
|
|
size_t const hills_energy_gradients_pos = is.tellg();
|
|
if (!(is >> key)) {
|
|
if (hills_energy_backup != NULL) {
|
|
delete hills_energy;
|
|
delete hills_energy_gradients;
|
|
hills_energy = hills_energy_backup;
|
|
hills_energy_gradients = hills_energy_gradients_backup;
|
|
}
|
|
is.clear();
|
|
is.seekg (hills_energy_gradients_pos, std::ios::beg);
|
|
is.setstate (std::ios::failbit);
|
|
return is;
|
|
} else if (!(key == std::string ("hills_energy_gradients")) ||
|
|
!(hills_energy_gradients->read_restart (is))) {
|
|
is.clear();
|
|
is.seekg (hills_energy_gradients_pos, std::ios::beg);
|
|
grids_from_restart_file = false;
|
|
if (!rebin_grids) {
|
|
if (hills_energy_backup == NULL)
|
|
cvm::fatal_error ("Error: couldn't read the free energy gradients grid for metadynamics bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
"; if useGrids was off when the state file was written, "
|
|
"enable rebinGrids now to regenerate the grids.\n");
|
|
else {
|
|
if (comm == single_replica)
|
|
cvm::log ("Error: couldn't read the free energy gradients grid for metadynamics bias \""+
|
|
this->name+"\".\n");
|
|
delete hills_energy;
|
|
delete hills_energy_gradients;
|
|
hills_energy = hills_energy_backup;
|
|
hills_energy_gradients = hills_energy_gradients_backup;
|
|
is.setstate (std::ios::failbit);
|
|
return is;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("Successfully read new grids for bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+"\n");
|
|
|
|
if (hills_energy_backup != NULL) {
|
|
// now that we have successfully updated the grids, delete the
|
|
// backup copies
|
|
if (cvm::debug())
|
|
cvm::log ("Deallocating the older grids.\n");
|
|
|
|
delete hills_energy_backup;
|
|
delete hills_energy_gradients_backup;
|
|
}
|
|
}
|
|
|
|
bool const existing_hills = (hills.size() > 0);
|
|
size_t const old_hills_size = hills.size();
|
|
hill_iter old_hills_end = hills.end();
|
|
hill_iter old_hills_off_grid_end = hills_off_grid.end();
|
|
|
|
// read the hills explicitly written (if there are any)
|
|
while (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 (grids_from_restart_file) {
|
|
if (hills.size() > old_hills_size)
|
|
cvm::log ("Read "+cvm::to_str (hills.size())+
|
|
" hills in addition to the grids.\n");
|
|
} else {
|
|
if (hills.size())
|
|
cvm::log ("Read "+cvm::to_str (hills.size())+" hills.\n");
|
|
}
|
|
|
|
if (rebin_grids) {
|
|
|
|
// allocate new grids (based on the new boundaries and widths just
|
|
// read from the configuration file), and project onto them the
|
|
// grids just read from the restart file
|
|
|
|
colvar_grid_scalar *new_hills_energy =
|
|
new colvar_grid_scalar (colvars);
|
|
colvar_grid_gradient *new_hills_energy_gradients =
|
|
new colvar_grid_gradient (colvars);
|
|
|
|
if (!grids_from_restart_file || (keep_hills && hills.size())) {
|
|
// if there are hills, recompute the new grids from them
|
|
cvm::log ("Rebinning the energy and forces grids from "+
|
|
cvm::to_str (hills.size())+" hills (this may take a while)...\n");
|
|
project_hills (hills.begin(), hills.end(),
|
|
new_hills_energy, new_hills_energy_gradients, true);
|
|
cvm::log ("rebinning done.\n");
|
|
|
|
} else {
|
|
// otherwise, use the grids in the restart file
|
|
cvm::log ("Rebinning the energy and forces grids "
|
|
"from the grids in the restart file.\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;
|
|
|
|
// assuming that some boundaries have expanded, eliminate those
|
|
// off-grid hills that aren't necessary any more
|
|
if (hills.size())
|
|
recount_hills_off_grid (hills.begin(), hills.end(), hills_energy);
|
|
}
|
|
|
|
if (use_grids) {
|
|
if (hills_off_grid.size()) {
|
|
cvm::log (cvm::to_str (hills_off_grid.size())+" hills are near the "
|
|
"grid boundaries: they will be computed analytically "
|
|
"and saved to the state files.\n");
|
|
}
|
|
}
|
|
|
|
is >> brace;
|
|
if (brace != "}") {
|
|
cvm::log ("Incomplete restart information for metadynamics bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
|
|
": no closing brace at position "+
|
|
cvm::to_str (is.tellg())+" in the file.\n");
|
|
is.setstate (std::ios::failbit);
|
|
return is;
|
|
}
|
|
|
|
if (cvm::debug())
|
|
cvm::log ("colvarbias_meta::read_restart() done\n");
|
|
|
|
if (existing_hills) {
|
|
hills.erase (hills.begin(), old_hills_end);
|
|
hills_off_grid.erase (hills_off_grid.begin(), old_hills_off_grid_end);
|
|
}
|
|
|
|
has_data = true;
|
|
|
|
if (comm != single_replica) {
|
|
read_replica_files();
|
|
}
|
|
|
|
return is;
|
|
}
|
|
|
|
|
|
std::istream & colvarbias_meta::read_hill (std::istream &is)
|
|
{
|
|
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;
|
|
}
|
|
|
|
size_t h_it;
|
|
get_keyval (data, "step", h_it, 0, parse_silent);
|
|
if (h_it <= state_file_step) {
|
|
if (cvm::debug())
|
|
cvm::log ("Skipping a hill older than the state file for metadynamics bias \""+
|
|
this->name+"\""+
|
|
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+"\n");
|
|
return is;
|
|
}
|
|
|
|
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;
|
|
// TODO: change this 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(), (std::sqrt (2.0 * PI) / 2.0)),
|
|
parse_silent);
|
|
|
|
std::string h_replica = "";
|
|
if (comm != single_replica) {
|
|
get_keyval (data, "replicaID", h_replica, replica_id, parse_silent);
|
|
if (h_replica != replica_id)
|
|
cvm::fatal_error ("Error: trying to read a hill created by replica \""+h_replica+
|
|
"\" for replica \""+replica_id+
|
|
"\"; did you swap output files?\n");
|
|
}
|
|
|
|
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) {
|
|
// if new_hills_begin is unset, set it for the first time
|
|
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, true);
|
|
if (min_dist < (3.0 * std::floor (hill_width)) + 1.0) {
|
|
hills_off_grid.push_back (hills.back());
|
|
}
|
|
}
|
|
|
|
has_data = true;
|
|
return is;
|
|
}
|
|
|
|
|
|
|
|
|
|
// **********************************************************************
|
|
// output functions
|
|
// **********************************************************************
|
|
|
|
std::ostream & colvarbias_meta::write_restart (std::ostream& os)
|
|
{
|
|
os << "metadynamics {\n"
|
|
<< " configuration {\n"
|
|
<< " step " << cvm::step_absolute() << "\n"
|
|
<< " name " << this->name << "\n";
|
|
if (this->comm != single_replica)
|
|
os << " replicaID " << this->replica_id << "\n";
|
|
os << " }\n\n";
|
|
|
|
if (use_grids) {
|
|
|
|
// this is a very good time to project hills, if you haven't done
|
|
// it already!
|
|
project_hills (new_hills_begin, hills.end(),
|
|
hills_energy, hills_energy_gradients);
|
|
new_hills_begin = hills.end();
|
|
|
|
// write down the grids to the restart file
|
|
os << " hills_energy\n";
|
|
hills_energy->write_restart (os);
|
|
os << " hills_energy_gradients\n";
|
|
hills_energy_gradients->write_restart (os);
|
|
}
|
|
|
|
if ( (!use_grids) || keep_hills ) {
|
|
// write all hills currently in memory
|
|
for (std::list<hill>::const_iterator h = this->hills.begin();
|
|
h != this->hills.end();
|
|
h++) {
|
|
os << *h;
|
|
}
|
|
} else {
|
|
// write just those that are near the grid boundaries
|
|
for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
|
|
h != this->hills_off_grid.end();
|
|
h++) {
|
|
os << *h;
|
|
}
|
|
}
|
|
|
|
os << "}\n\n";
|
|
|
|
if (comm != single_replica) {
|
|
write_replica_state_file();
|
|
// schedule to reread the state files of the other replicas (they
|
|
// have also rewritten them)
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
(replicas[ir])->replica_state_file_in_sync = false;
|
|
}
|
|
}
|
|
|
|
if (dump_fes) {
|
|
write_pmf();
|
|
}
|
|
|
|
return os;
|
|
}
|
|
|
|
|
|
void colvarbias_meta::write_pmf()
|
|
{
|
|
// allocate a new grid to store the pmf
|
|
colvar_grid_scalar *pmf = new colvar_grid_scalar (colvars);
|
|
|
|
std::string fes_file_name_prefix (cvm::output_prefix);
|
|
|
|
if ((cvm::n_meta_biases > 1) || (cvm::n_abf_biases > 0)) {
|
|
// if this is not the only free energy integrator, append
|
|
// this bias's name, to distinguish it from the output of the other
|
|
// biases producing a .pmf file
|
|
// TODO: fix for ABF with updateBias == no
|
|
fes_file_name_prefix += ("."+this->name);
|
|
}
|
|
|
|
if ((comm == single_replica) || (dump_replica_fes)) {
|
|
// output the PMF from this instance or replica
|
|
pmf->reset();
|
|
pmf->add_grid (*hills_energy);
|
|
cvm::real const max = pmf->maximum_value();
|
|
pmf->add_constant (-1.0 * max);
|
|
pmf->multiply_constant (-1.0);
|
|
if (well_tempered) {
|
|
cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature;
|
|
pmf->multiply_constant (well_temper_scale);
|
|
}
|
|
std::string const fes_file_name (fes_file_name_prefix +
|
|
((comm != single_replica) ? ".partial" : "") +
|
|
(dump_fes_save ?
|
|
"."+cvm::to_str (cvm::step_absolute()) : "") +
|
|
".pmf");
|
|
cvm::backup_file (fes_file_name.c_str());
|
|
std::ofstream fes_os (fes_file_name.c_str());
|
|
pmf->write_multicol (fes_os);
|
|
fes_os.close();
|
|
}
|
|
|
|
if (comm != single_replica) {
|
|
// output the combined PMF from all replicas
|
|
pmf->reset();
|
|
pmf->add_grid (*hills_energy);
|
|
for (size_t ir = 0; ir < replicas.size(); ir++) {
|
|
pmf->add_grid (*(replicas[ir]->hills_energy));
|
|
}
|
|
cvm::real const max = pmf->maximum_value();
|
|
pmf->add_constant (-1.0 * max);
|
|
pmf->multiply_constant (-1.0);
|
|
if (well_tempered) {
|
|
cvm::real const well_temper_scale = (bias_temperature + cvm::temperature()) / bias_temperature;
|
|
pmf->multiply_constant (well_temper_scale);
|
|
}
|
|
std::string const fes_file_name (fes_file_name_prefix +
|
|
(dump_fes_save ?
|
|
"."+cvm::to_str (cvm::step_absolute()) : "") +
|
|
".pmf");
|
|
cvm::backup_file (fes_file_name.c_str());
|
|
std::ofstream fes_os (fes_file_name.c_str());
|
|
pmf->write_multicol (fes_os);
|
|
fes_os.close();
|
|
}
|
|
|
|
delete pmf;
|
|
}
|
|
|
|
|
|
|
|
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());
|
|
if (!rep_state_os.good())
|
|
cvm::fatal_error ("Error: in opening file \""+
|
|
replica_state_file+"\" for writing.\n");
|
|
|
|
rep_state_os.setf (std::ios::scientific, std::ios::floatfield);
|
|
rep_state_os << "\n"
|
|
<< "metadynamics {\n"
|
|
<< " configuration {\n"
|
|
<< " name " << this->name << "\n"
|
|
<< " step " << cvm::step_absolute() << "\n";
|
|
if (this->comm != single_replica) {
|
|
rep_state_os << " replicaID " << this->replica_id << "\n";
|
|
}
|
|
rep_state_os << " }\n\n";
|
|
rep_state_os << " hills_energy\n";
|
|
rep_state_os << std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width);
|
|
hills_energy->write_restart (rep_state_os);
|
|
rep_state_os << " hills_energy_gradients\n";
|
|
rep_state_os << std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width);
|
|
hills_energy_gradients->write_restart (rep_state_os);
|
|
|
|
if ( (!use_grids) || keep_hills ) {
|
|
// write all hills currently in memory
|
|
for (std::list<hill>::const_iterator h = this->hills.begin();
|
|
h != this->hills.end();
|
|
h++) {
|
|
rep_state_os << *h;
|
|
}
|
|
} else {
|
|
// write just those that are near the grid boundaries
|
|
for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
|
|
h != this->hills_off_grid.end();
|
|
h++) {
|
|
rep_state_os << *h;
|
|
}
|
|
}
|
|
|
|
rep_state_os << "}\n\n";
|
|
rep_state_os.close();
|
|
|
|
// reopen the hills file
|
|
replica_hills_os.close();
|
|
replica_hills_os.open (replica_hills_file.c_str());
|
|
if (!replica_hills_os.good())
|
|
cvm::fatal_error ("Error: in opening file \""+
|
|
replica_hills_file+"\" for writing.\n");
|
|
replica_hills_os.setf (std::ios::scientific, std::ios::floatfield);
|
|
}
|
|
|
|
std::string colvarbias_meta::hill::output_traj()
|
|
{
|
|
std::ostringstream os;
|
|
os.setf (std::ios::fixed, std::ios::floatfield);
|
|
os << std::setw (cvm::it_width) << it << " ";
|
|
|
|
os.setf (std::ios::scientific, std::ios::floatfield);
|
|
|
|
os << " ";
|
|
for (size_t i = 0; i < centers.size(); i++) {
|
|
os << " ";
|
|
os << std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width) << centers[i];
|
|
}
|
|
|
|
os << " ";
|
|
for (size_t i = 0; i < widths.size(); i++) {
|
|
os << " ";
|
|
os << std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width) << widths[i];
|
|
}
|
|
|
|
os << " ";
|
|
os << std::setprecision (cvm::en_prec)
|
|
<< std::setw (cvm::en_width) << W << "\n";
|
|
|
|
return os.str();
|
|
}
|
|
|
|
|
|
std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
|
|
{
|
|
os.setf (std::ios::scientific, std::ios::floatfield);
|
|
|
|
os << "hill {\n";
|
|
os << " step " << std::setw (cvm::it_width) << h.it << "\n";
|
|
os << " weight "
|
|
<< std::setprecision (cvm::en_prec)
|
|
<< std::setw (cvm::en_width)
|
|
<< h.W << "\n";
|
|
|
|
if (h.replica.size())
|
|
os << " replicaID " << h.replica << "\n";
|
|
|
|
os << " centers ";
|
|
for (size_t i = 0; i < (h.centers).size(); i++) {
|
|
os << " "
|
|
<< std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width)
|
|
<< h.centers[i];
|
|
}
|
|
os << "\n";
|
|
|
|
os << " widths ";
|
|
for (size_t i = 0; i < (h.widths).size(); i++) {
|
|
os << " "
|
|
<< std::setprecision (cvm::cv_prec)
|
|
<< std::setw (cvm::cv_width)
|
|
<< h.widths[i];
|
|
}
|
|
os << "\n";
|
|
|
|
os << "}\n";
|
|
|
|
return os;
|
|
}
|