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Use smart pointers to manage metadynamics grid data
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@giacomofiorin
giacomofiorin committed Oct 18, 2024
1 parent 617731a commit 830be00
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Showing 2 changed files with 46 additions and 47 deletions.
82 changes: 40 additions & 42 deletions src/colvarbias_meta.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvar.h"
#include "colvargrid.h"
#include "colvarbias_meta.h"
#include "colvars_memstream.h"

Expand All @@ -31,8 +32,6 @@ colvarbias_meta::colvarbias_meta(char const *key)
use_grids = true;
grids_freq = 0;
rebin_grids = false;
hills_energy = NULL;
hills_energy_gradients = NULL;

dump_fes = true;
keep_hills = false;
Expand Down Expand Up @@ -143,9 +142,9 @@ int colvarbias_meta::init(std::string const &conf)
get_keyval(conf, "keepHills", keep_hills, keep_hills);
get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save);

if (hills_energy == NULL) {
hills_energy = new colvar_grid_scalar(colvars);
hills_energy_gradients = new colvar_grid_gradient(colvars);
if (!hills_energy) {
hills_energy.reset(new colvar_grid_scalar(colvars));
hills_energy_gradients.reset(new colvar_grid_gradient(colvars));
}

} else {
Expand Down Expand Up @@ -254,7 +253,6 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
{
int error_code = COLVARS_OK;
// for ebmeta
target_dist = NULL;
get_keyval(conf, "ebMeta", ebmeta, false);
if(ebmeta){
cvm::main()->cite_feature("Ensemble-biased metadynamics (ebMetaD)");
Expand All @@ -265,7 +263,7 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
"targetDistFile accordingly.\n",
COLVARS_INPUT_ERROR);
}
target_dist = new colvar_grid_scalar();
target_dist.reset(new colvar_grid_scalar());
error_code |= target_dist->init_from_colvars(colvars);
std::string target_dist_file;
get_keyval(conf, "targetDistFile", target_dist_file);
Expand Down Expand Up @@ -523,10 +521,8 @@ int colvarbias_meta::update_grid_params()
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;
hills_energy.reset(new_hills_energy);
hills_energy_gradients.reset(new_hills_energy_gradients);

curr_bin = hills_energy->get_colvars_index();
if (cvm::debug())
Expand Down Expand Up @@ -1061,8 +1057,8 @@ int colvarbias_meta::update_replicas_registry()
(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);
(replicas.back())->hills_energy.reset(new colvar_grid_scalar(colvars));
(replicas.back())->hills_energy_gradients.reset(new colvar_grid_gradient(colvars));
}
if (is_enabled(f_cvb_calc_ti_samples)) {
(replicas.back())->enable(f_cvb_calc_ti_samples);
Expand Down Expand Up @@ -1319,34 +1315,40 @@ template <typename IST> IST &colvarbias_meta::read_state_data_template_(IST &is)
{
if (use_grids) {

colvar_grid_scalar *hills_energy_backup = NULL;
colvar_grid_gradient *hills_energy_gradients_backup = NULL;
std::unique_ptr<colvar_grid_scalar> hills_energy_backup;
std::unique_ptr<colvar_grid_gradient> hills_energy_gradients_backup;

if (has_data) {
bool const need_backup = has_data;

if (need_backup) {
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);
cvm::log("Backing up grids for metadynamics bias \"" + this->name + "\"" +
((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + ".\n");

hills_energy_backup = std::move(hills_energy);
hills_energy_gradients_backup = std::move(hills_energy_gradients);
hills_energy.reset(new colvar_grid_scalar(colvars));
hills_energy_gradients.reset(new colvar_grid_gradient(colvars));
}

read_grid_data_template_<IST, colvar_grid_scalar>(is, "hills_energy", hills_energy,
hills_energy_backup);
read_grid_data_template_<IST, colvar_grid_scalar>(is, "hills_energy", hills_energy.get(),
hills_energy_backup.get());

read_grid_data_template_<IST, colvar_grid_gradient>(
is, "hills_energy_gradients", hills_energy_gradients, hills_energy_gradients_backup);
read_grid_data_template_<IST, colvar_grid_gradient>(is, "hills_energy_gradients",
hills_energy_gradients.get(),
hills_energy_gradients_backup.get());

if (is) {
cvm::log(" successfully read the biasing potential and its gradients from grids.\n");
if (hills_energy_backup != nullptr) {
// Now that we have successfully updated the grids, delete the backup copies
delete hills_energy_backup;
delete hills_energy_gradients_backup;
}
} else {
if (need_backup) {
if (cvm::debug())
cvm::log("Restoring grids from backup for metadynamics bias \"" + this->name + "\"" +
((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + ".\n");
// Restoring content from original grid
hills_energy->copy_grid(*hills_energy_backup);
hills_energy_gradients->copy_grid(*hills_energy_gradients_backup);
}
return is;
}
}
Expand Down Expand Up @@ -1434,10 +1436,8 @@ void colvarbias_meta::rebin_grids_after_restart()
// 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);
std::unique_ptr<colvar_grid_scalar> new_hills_energy(new colvar_grid_scalar(colvars));
std::unique_ptr<colvar_grid_gradient> new_hills_energy_gradients(new colvar_grid_gradient(colvars));

if (cvm::debug()) {
std::ostringstream tmp_os;
Expand All @@ -1464,15 +1464,13 @@ void colvarbias_meta::rebin_grids_after_restart()
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;
hills_energy = std::move(new_hills_energy);
hills_energy_gradients = std::move(new_hills_energy_gradients);

// assuming that some boundaries have expanded, eliminate those
// off-grid hills that aren't necessary any more
if (!hills.empty())
recount_hills_off_grid(hills.begin(), hills.end(), hills_energy);
recount_hills_off_grid(hills.begin(), hills.end());
}
}

Expand Down Expand Up @@ -1813,7 +1811,7 @@ template <typename OST> OST &colvarbias_meta::write_state_data_template_(OST &os

// 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);
project_hills(new_hills_begin, hills.end(), hills_energy.get(), hills_energy_gradients.get());
new_hills_begin = hills.end();

// write down the grids to the restart file
Expand Down
11 changes: 6 additions & 5 deletions src/colvarbias_meta.h
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,10 @@
#ifndef COLVARBIAS_META_H
#define COLVARBIAS_META_H

#include <vector>
#include <list>
#include <iosfwd>
#include <list>
#include <memory>
#include <vector>

#include "colvarbias.h"

Expand Down Expand Up @@ -213,7 +214,7 @@ class colvarbias_meta
bool ebmeta;

/// Target distribution for EBmeta
std::shared_ptr<colvar_grid_scalar> target_dist;
std::unique_ptr<colvar_grid_scalar> target_dist;

/// Number of equilibration steps for EBmeta
cvm::step_number ebmeta_equil_steps;
Expand All @@ -225,10 +226,10 @@ class colvarbias_meta
bool safely_read_restart;

/// Hill energy, cached on a grid
std::shared_ptr<colvar_grid_scalar> hills_energy;
std::unique_ptr<colvar_grid_scalar> hills_energy;

/// Hill forces, cached on a grid
std::shared_ptr<colvar_grid_gradient> hills_energy_gradients;
std::unique_ptr<colvar_grid_gradient> hills_energy_gradients;

/// Project the selected hills onto grids
void project_hills(hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge,
Expand Down

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