Update Colvars library to version 2023-05-01
This update consists exclusively of bugfixes or maintenance-related changes. The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS: - 532 Add XYZ trajectory reading feature https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin) - 531 Delete objects quietly, unless explicitly requested via script (including VMD) https://github.com/Colvars/colvars/pull/531 (@giacomofiorin) - 530 Append newline to log and error messages if not already present https://github.com/Colvars/colvars/pull/530 (@giacomofiorin) - 528 Forward-declare OpenMP lock https://github.com/Colvars/colvars/pull/528 (@giacomofiorin) - 527 Remove unneeded STL container https://github.com/Colvars/colvars/pull/527 (@giacomofiorin) - 526 Allow collecting configuration files and strings before setting up interface https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin) - 523 Fallback to linearCombination when customFunction is missing in customColvar https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin) - 522 Use iostream::fail() to check for I/O error https://github.com/Colvars/colvars/pull/522 (@jhenin) - 520 Fix ref count https://github.com/Colvars/colvars/pull/520 (@giacomofiorin) - 513 Set target temperature through a common code path https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin) - 509 Safer detection of Windows with recent Microsoft Visual Studio versions https://github.com/Colvars/colvars/pull/509 (@akohlmey) - 508 Update LAMMPS patching method to reflect Lepton availability https://github.com/Colvars/colvars/pull/508 (@giacomofiorin) - 497 Increase the precision of write_multicol https://github.com/Colvars/colvars/pull/497 (@HanatoK) - 496 Only perform MTS automatic enable/disable for timeStepFactor > 1 https://github.com/Colvars/colvars/pull/496 (@giacomofiorin) - 493 Remove unused branch of quaternion input function https://github.com/Colvars/colvars/pull/493 (@giacomofiorin) - 489 Ensure there are spaces between the fields in the header https://github.com/Colvars/colvars/pull/489 (@HanatoK) - 487 Use map of output streams, and return references to its elements https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin) - 486 Remember first step of moving restraint https://github.com/Colvars/colvars/pull/486 (@jhenin) - 485 Add decoupling option for moving restraints https://github.com/Colvars/colvars/pull/485 (@jhenin) - 483 Update Lepton via patching procedure https://github.com/Colvars/colvars/pull/483 (@giacomofiorin) - 481 Make file-reading operations of input data abstractable https://github.com/Colvars/colvars/pull/481 (@giacomofiorin) Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
@ -36,7 +36,6 @@ colvarbias_meta::colvarbias_meta(char const *key)
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: colvarbias(key), colvarbias_ti(key)
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{
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new_hills_begin = hills.end();
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hills_traj_os = NULL;
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hill_weight = 0.0;
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hill_width = 0.0;
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@ -268,28 +267,31 @@ int colvarbias_meta::init_well_tempered_params(std::string const &conf)
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int colvarbias_meta::init_ebmeta_params(std::string const &conf)
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{
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int error_code = COLVARS_OK;
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// for ebmeta
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target_dist = NULL;
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get_keyval(conf, "ebMeta", ebmeta, false);
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if(ebmeta){
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cvm::main()->cite_feature("Ensemble-biased metadynamics (ebMetaD)");
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if (use_grids && expand_grids) {
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cvm::error("Error: expandBoundaries is not supported with "
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"ebMeta please allocate wide enough boundaries for "
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"each colvar ahead of time and set targetdistfile "
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"accordingly.\n", COLVARS_INPUT_ERROR);
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error_code |= cvm::error("Error: expandBoundaries is not supported with "
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"ebMeta; please allocate wide enough boundaries "
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"for each colvar ahead of time and set "
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"targetDistFile accordingly.\n",
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COLVARS_INPUT_ERROR);
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}
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target_dist = new colvar_grid_scalar();
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target_dist->init_from_colvars(colvars);
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error_code |= target_dist->init_from_colvars(colvars);
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std::string target_dist_file;
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get_keyval(conf, "targetDistFile", target_dist_file);
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std::ifstream targetdiststream(target_dist_file.c_str());
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target_dist->read_multicol(targetdiststream);
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error_code |= target_dist->read_multicol(target_dist_file,
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"ebMeta target histogram");
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cvm::real min_val = target_dist->minimum_value();
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cvm::real max_val = target_dist->maximum_value();
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if(min_val<0){
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cvm::error("Error: Target distribution of EBMetaD "
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"has negative values!.\n", COLVARS_INPUT_ERROR);
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if (min_val < 0.0) {
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error_code |= cvm::error("Error: Target distribution of EBMetaD "
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"has negative values!.\n",
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COLVARS_INPUT_ERROR);
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}
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cvm::real target_dist_min_val;
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get_keyval(conf, "targetDistMinVal", target_dist_min_val, 1/1000000.0);
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@ -301,17 +303,19 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
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cvm::log("NOTE: targetDistMinVal is set to zero, the minimum value of the target \n");
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cvm::log(" distribution will be set as the minimum positive value.\n");
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cvm::real min_pos_val = target_dist->minimum_pos_value();
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if(min_pos_val<=0){
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cvm::error("Error: Target distribution of EBMetaD has negative "
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"or zero minimum positive value!.\n", COLVARS_INPUT_ERROR);
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if (min_pos_val <= 0.0){
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error_code |= cvm::error("Error: Target distribution of EBMetaD has "
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"negative or zero minimum positive value.\n",
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COLVARS_INPUT_ERROR);
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}
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if(min_val==0){
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if (min_val == 0.0){
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cvm::log("WARNING: Target distribution has zero values.\n");
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cvm::log("Zeros will be converted to the minimum positive value.\n");
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target_dist->remove_small_values(min_pos_val);
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}
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} else {
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cvm::error("Error: targetDistMinVal must be a value between 0 and 1!.\n", COLVARS_INPUT_ERROR);
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error_code |= cvm::error("Error: targetDistMinVal must be a value "
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"between 0 and 1.\n", COLVARS_INPUT_ERROR);
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}
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}
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// normalize target distribution and multiply by effective volume = exp(differential entropy)
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@ -321,23 +325,18 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
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get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, ebmeta_equil_steps);
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}
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return COLVARS_OK;
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return error_code;
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}
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colvarbias_meta::~colvarbias_meta()
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{
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colvarbias_meta::clear_state_data();
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colvarproxy *proxy = cvm::proxy;
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colvarproxy *proxy = cvm::main()->proxy;
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if (proxy->get_output_stream(replica_hills_file)) {
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proxy->close_output_stream(replica_hills_file);
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}
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proxy->close_output_stream(replica_hills_file);
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if (hills_traj_os) {
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proxy->close_output_stream(hills_traj_file_name());
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hills_traj_os = NULL;
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}
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proxy->close_output_stream(hills_traj_file_name());
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if (target_dist) {
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delete target_dist;
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@ -392,9 +391,12 @@ colvarbias_meta::add_hill(colvarbias_meta::hill const &h)
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}
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// output to trajectory (if specified)
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if (hills_traj_os) {
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*hills_traj_os << (hills.back()).output_traj();
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cvm::proxy->flush_output_stream(hills_traj_os);
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if (b_hills_traj) {
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// Open trajectory file or access the one already open
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std::ostream &hills_traj_os =
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cvm::proxy->output_stream(hills_traj_file_name());
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hills_traj_os << (hills.back()).output_traj();
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cvm::proxy->flush_output_stream(hills_traj_file_name());
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}
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has_data = true;
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@ -424,12 +426,14 @@ colvarbias_meta::delete_hill(hill_iter &h)
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}
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}
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if (hills_traj_os) {
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if (b_hills_traj) {
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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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cvm::proxy->flush_output_stream(hills_traj_os);
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std::ostream &hills_traj_os =
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cvm::proxy->output_stream(hills_traj_file_name());
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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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cvm::proxy->flush_output_stream(hills_traj_file_name());
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}
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return hills.erase(h);
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@ -573,6 +577,7 @@ int colvarbias_meta::update_grid_params()
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int colvarbias_meta::update_bias()
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{
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colvarproxy *proxy = cvm::main()->proxy;
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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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can_accumulate_data() && is_enabled(f_cvb_history_dependent)) {
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@ -603,7 +608,7 @@ int colvarbias_meta::update_bias()
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} else {
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calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here, NULL);
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}
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hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
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hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*proxy->boltzmann()));
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}
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switch (comm) {
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@ -618,10 +623,10 @@ int colvarbias_meta::update_bias()
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case multiple_replicas:
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add_hill(hill(cvm::step_absolute(), hill_weight*hills_scale,
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colvar_values, colvar_sigmas, replica_id));
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std::ostream *replica_hills_os =
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cvm::proxy->get_output_stream(replica_hills_file);
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std::ostream &replica_hills_os =
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cvm::proxy->output_stream(replica_hills_file);
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if (replica_hills_os) {
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*replica_hills_os << hills.back();
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replica_hills_os << hills.back();
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} else {
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return cvm::error("Error: in metadynamics bias \""+this->name+"\""+
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((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
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@ -979,25 +984,24 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first
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int colvarbias_meta::replica_share()
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{
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int error_code = COLVARS_OK;
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colvarproxy *proxy = cvm::proxy;
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// sync with the other replicas (if needed)
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if (comm == multiple_replicas) {
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// reread the replicas registry
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update_replicas_registry();
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error_code |= update_replicas_registry();
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// empty the output buffer
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std::ostream *replica_hills_os =
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proxy->get_output_stream(replica_hills_file);
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if (replica_hills_os) {
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proxy->flush_output_stream(replica_hills_os);
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}
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read_replica_files();
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error_code |= proxy->flush_output_stream(replica_hills_file);
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error_code |= read_replica_files();
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}
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return COLVARS_OK;
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return error_code;
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}
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void colvarbias_meta::update_replicas_registry()
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int colvarbias_meta::update_replicas_registry()
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{
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int error_code = COLVARS_OK;
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if (cvm::debug())
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cvm::log("Metadynamics bias \""+this->name+"\""+
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": updating the list of replicas, currently containing "+
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@ -1012,8 +1016,9 @@ void colvarbias_meta::update_replicas_registry()
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while (colvarparse::getline_nocomments(reg_file, line))
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replicas_registry.append(line+"\n");
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} else {
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cvm::error("Error: failed to open file \""+replicas_registry_file+
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"\" for reading.\n", COLVARS_FILE_ERROR);
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error_code |= cvm::error("Error: failed to open file \""+
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replicas_registry_file+"\" for reading.\n",
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COLVARS_FILE_ERROR);
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}
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}
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@ -1081,8 +1086,8 @@ void colvarbias_meta::update_replicas_registry()
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}
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}
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} else {
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cvm::error("Error: cannot read the replicas registry file \""+
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replicas_registry+"\".\n", COLVARS_FILE_ERROR);
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error_code |= cvm::error("Error: cannot read the replicas registry file \""+
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replicas_registry+"\".\n", COLVARS_FILE_ERROR);
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}
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// now (re)read the list file of each replica
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@ -1122,10 +1127,12 @@ void colvarbias_meta::update_replicas_registry()
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if (cvm::debug())
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cvm::log("Metadynamics bias \""+this->name+"\": the list of replicas contains "+
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cvm::to_str(replicas.size())+" elements.\n");
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return error_code;
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}
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void colvarbias_meta::read_replica_files()
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int colvarbias_meta::read_replica_files()
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{
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// Note: we start from the 2nd replica.
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for (size_t ir = 1; ir < replicas.size(); ir++) {
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@ -1250,6 +1257,7 @@ void colvarbias_meta::read_replica_files()
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" steps. Ensure that it is still running.\n");
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}
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}
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return COLVARS_OK;
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}
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@ -1413,6 +1421,10 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
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size_t const old_hills_size = hills.size();
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hill_iter old_hills_end = hills.end();
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hill_iter old_hills_off_grid_end = hills_off_grid.end();
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if (cvm::debug()) {
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cvm::log("Before reading hills from the state file, there are "+
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cvm::to_str(hills.size())+" hills in memory.\n");
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}
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// Read any hills following the grid data (if any)
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while (read_hill(is)) {
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@ -1431,6 +1443,10 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
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if (existing_hills) {
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hills.erase(hills.begin(), old_hills_end);
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hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end);
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if (cvm::debug()) {
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cvm::log("After pruning the old hills, there are now "+
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cvm::to_str(hills.size())+" hills in memory.\n");
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}
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}
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if (rebin_grids) {
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@ -1614,6 +1630,8 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
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int colvarbias_meta::setup_output()
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{
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int error_code = COLVARS_OK;
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output_prefix = cvm::output_prefix();
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if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) > 1) {
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// if this is not the only free energy integrator, append
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@ -1626,8 +1644,11 @@ int colvarbias_meta::setup_output()
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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::error("Error: cannot get the path of the current working directory.\n");
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if (GETCWD(pwd, 3000) == NULL) {
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return cvm::error("Error: cannot get the path of the current working directory.\n",
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COLVARS_BUG_ERROR);
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}
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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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@ -1680,38 +1701,35 @@ int colvarbias_meta::setup_output()
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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::ostream *list_os =
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cvm::proxy->output_stream(replica_list_file,
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(use_grids ? std::ios_base::trunc :
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std::ios_base::app));
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if (!list_os) {
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return cvm::get_error();
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std::ostream &list_os = cvm::proxy->output_stream(replica_list_file);
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if (list_os) {
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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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cvm::proxy->close_output_stream(replica_list_file);
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} else {
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error_code |= COLVARS_FILE_ERROR;
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}
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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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cvm::proxy->close_output_stream(replica_list_file);
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// finally, add a new record for this replica to the registry
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if (! registered_replica) {
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std::ostream *reg_os =
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cvm::proxy->output_stream(replicas_registry_file,
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std::ios::app);
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std::ofstream reg_os(replicas_registry_file.c_str(), std::ios::app);
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if (!reg_os) {
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return cvm::get_error();
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}
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*reg_os << replica_id << " " << replica_list_file << "\n";
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reg_os << replica_id << " " << replica_list_file << "\n";
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cvm::proxy->close_output_stream(replicas_registry_file);
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}
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}
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if (b_hills_traj) {
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std::ostream &hills_traj_os =
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cvm::proxy->output_stream(hills_traj_file_name());
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if (!hills_traj_os) {
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hills_traj_os = cvm::proxy->output_stream(hills_traj_file_name());
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if (!hills_traj_os) return cvm::get_error();
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error_code |= COLVARS_FILE_ERROR;
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}
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}
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return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
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return error_code;
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}
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@ -1804,6 +1822,7 @@ int colvarbias_meta::write_output_files()
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void colvarbias_meta::write_pmf()
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{
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colvarproxy *proxy = cvm::main()->proxy;
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// allocate a new grid to store the pmf
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colvar_grid_scalar *pmf = new colvar_grid_scalar(*hills_energy);
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pmf->setup();
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@ -1820,7 +1839,7 @@ void colvarbias_meta::write_pmf()
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cvm::real target_val=target_dist->value(i);
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if (target_val>0) {
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pmf_val=pmf->value(i);
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pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
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pmf_val=pmf_val + proxy->target_temperature() * proxy->boltzmann() * cvm::logn(target_val);
|
||||
}
|
||||
pmf->set_value(i,pmf_val);
|
||||
}
|
||||
@ -1830,7 +1849,7 @@ void colvarbias_meta::write_pmf()
|
||||
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;
|
||||
cvm::real const well_temper_scale = (bias_temperature + proxy->target_temperature()) / bias_temperature;
|
||||
pmf->multiply_constant(well_temper_scale);
|
||||
}
|
||||
{
|
||||
@ -1839,10 +1858,7 @@ void colvarbias_meta::write_pmf()
|
||||
(dump_fes_save ?
|
||||
"."+cvm::to_str(cvm::step_absolute()) : "") +
|
||||
".pmf");
|
||||
cvm::proxy->backup_file(fes_file_name);
|
||||
std::ostream *fes_os = cvm::proxy->output_stream(fes_file_name);
|
||||
pmf->write_multicol(*fes_os);
|
||||
cvm::proxy->close_output_stream(fes_file_name);
|
||||
pmf->write_multicol(fes_file_name, "PMF file");
|
||||
}
|
||||
}
|
||||
|
||||
@ -1861,7 +1877,7 @@ void colvarbias_meta::write_pmf()
|
||||
cvm::real target_val=target_dist->value(i);
|
||||
if (target_val>0) {
|
||||
pmf_val=pmf->value(i);
|
||||
pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
|
||||
pmf_val=pmf_val + proxy->target_temperature() * proxy->boltzmann() * cvm::logn(target_val);
|
||||
}
|
||||
pmf->set_value(i,pmf_val);
|
||||
}
|
||||
@ -1871,17 +1887,14 @@ void colvarbias_meta::write_pmf()
|
||||
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;
|
||||
cvm::real const well_temper_scale = (bias_temperature + proxy->target_temperature()) / bias_temperature;
|
||||
pmf->multiply_constant(well_temper_scale);
|
||||
}
|
||||
std::string const fes_file_name(this->output_prefix +
|
||||
(dump_fes_save ?
|
||||
"."+cvm::to_str(cvm::step_absolute()) : "") +
|
||||
".pmf");
|
||||
cvm::proxy->backup_file(fes_file_name);
|
||||
std::ostream *fes_os = cvm::proxy->output_stream(fes_file_name);
|
||||
pmf->write_multicol(*fes_os);
|
||||
cvm::proxy->close_output_stream(fes_file_name);
|
||||
pmf->write_multicol(fes_file_name, "partial PMF file");
|
||||
}
|
||||
|
||||
delete pmf;
|
||||
@ -1902,9 +1915,9 @@ int colvarbias_meta::write_replica_state_file()
|
||||
// Write to temporary state file
|
||||
std::string const tmp_state_file(replica_state_file+".tmp");
|
||||
error_code |= proxy->remove_file(tmp_state_file);
|
||||
std::ostream *rep_state_os = cvm::proxy->output_stream(tmp_state_file);
|
||||
std::ostream &rep_state_os = cvm::proxy->output_stream(tmp_state_file);
|
||||
if (rep_state_os) {
|
||||
if (!write_state(*rep_state_os)) {
|
||||
if (!write_state(rep_state_os)) {
|
||||
error_code |= cvm::error("Error: in writing to temporary file \""+
|
||||
tmp_state_file+"\".\n", COLVARS_FILE_ERROR);
|
||||
}
|
||||
@ -1921,13 +1934,13 @@ int colvarbias_meta::reopen_replica_buffer_file()
|
||||
{
|
||||
int error_code = COLVARS_OK;
|
||||
colvarproxy *proxy = cvm::proxy;
|
||||
if (proxy->get_output_stream(replica_hills_file) != NULL) {
|
||||
if (proxy->output_stream(replica_hills_file)) {
|
||||
error_code |= proxy->close_output_stream(replica_hills_file);
|
||||
}
|
||||
error_code |= proxy->remove_file(replica_hills_file);
|
||||
std::ostream *replica_hills_os = proxy->output_stream(replica_hills_file);
|
||||
std::ostream &replica_hills_os = proxy->output_stream(replica_hills_file);
|
||||
if (replica_hills_os) {
|
||||
replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
|
||||
replica_hills_os.setf(std::ios::scientific, std::ios::floatfield);
|
||||
} else {
|
||||
error_code |= COLVARS_FILE_ERROR;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user