Skip to content

Commit

Permalink
Modified implementation of interval in calc_energy and calc_forces
Browse files Browse the repository at this point in the history 
by using get_colvar_index_bound to treat vaules out of the boundary (which are projected inside the closest boundary).
Additionally curr_values are now defined as a general variable to avoid define a new variable every time
functions are called
  • Loading branch information
@fabsugar @giacomofiorin
fabsugar authored and giacomofiorin committed Apr 19, 2023
1 parent 59c0047 commit 010d8a4
Show file tree
Hide file tree
Showing 3 changed files with 33 additions and 63 deletions.
82 changes: 19 additions & 63 deletions src/colvarbias_meta.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -569,6 +569,11 @@ int colvarbias_meta::init_interval_params(std::string const &conf)
std::vector<int> interval_ulimit_cv;
size_t i;
size_t j;
// allocate accessory variable of colvar values to be used in energy and forces calculation
curr_values.resize(num_variables());
for (i = 0; i < num_variables(); i++) {
curr_values[i].type(variables(i)->value());
}

if (get_keyval(conf, "useHillsInterval", use_interval, use_interval)) {
if (use_interval) {
Expand Down Expand Up @@ -1220,11 +1225,7 @@ int colvarbias_meta::calc_energy(std::vector<colvarvalue> const *values)

size_t i;
int ii;
cvm::real up_bound_bin_value;
std::vector<colvarvalue> curr_values(num_variables());
for (i = 0; i < num_variables(); i++) {
curr_values[i].type(variables(i)->value());
}
std::vector<int> curr_bin;

curr_values = values ? *values : colvar_values;

Expand All @@ -1235,25 +1236,19 @@ int colvarbias_meta::calc_energy(std::vector<colvarvalue> const *values)
curr_values[i]=interval_llimit[ii];
}
ii=which_int_ulimit_cv[i];
if (ii>-1 && curr_values[i]>=interval_ulimit[ii] ) {
// check if upper border is out of the grid otherwise put it back on the grid
up_bound_bin_value=hills_energy->lower_boundaries[i].real_value+variables(i)->width*(0.5+cvm::floor((interval_ulimit[ii]-hills_energy->lower_boundaries[i].real_value)/variables(i)->width));
//if (interval_ulimit[ii]==hills_energy->upper_boundaries[i].real_value){
if (up_bound_bin_value>hills_energy->upper_boundaries[i].real_value) {
curr_values[i]=interval_ulimit[ii]-0.5*(variables(i)->width); // upper border is out of grid; in this way is in
} else {
curr_values[i]=interval_ulimit[ii];
}
if (ii>-1 && curr_values[i]>interval_ulimit[ii] ) {
curr_values[i]=interval_ulimit[ii];
}
}
curr_bin = hills_energy->get_colvars_index_bound(curr_values);
} else {
curr_bin = hills_energy->get_colvars_index(curr_values);
}

for (ir = 0; ir < replicas.size(); ir++) {
replicas[ir]->bias_energy = 0.0;
}

std::vector<int> const curr_bin = hills_energy->get_colvars_index(curr_values);

if (hills_energy->index_ok(curr_bin)) {
// index is within the grid: get the energy from there
for (ir = 0; ir < replicas.size(); ir++) {
Expand Down Expand Up @@ -1282,20 +1277,6 @@ int colvarbias_meta::calc_energy(std::vector<colvarvalue> const *values)
// now include the hills that have not been binned yet (starting
// from new_hills_begin)

if (use_interval) {
curr_values = values ? *values : colvar_values;
for (i = 0; i < num_variables(); i++) {
ii=which_int_llimit_cv[i];
if (ii>-1 && curr_values[i]<interval_llimit[ii] ) {
curr_values[i]=interval_llimit[ii];
}
ii=which_int_ulimit_cv[i];
if (ii>-1 && curr_values[i]>interval_ulimit[ii] ) {
curr_values[i]=interval_ulimit[ii];
}
}
}

for (ir = 0; ir < replicas.size(); ir++) {
calc_hills(replicas[ir]->new_hills_begin,
replicas[ir]->hills.end(),
Expand All @@ -1314,11 +1295,7 @@ int colvarbias_meta::calc_forces(std::vector<colvarvalue> const *values)
{
size_t ir = 0, ic = 0;
int ii;
cvm::real up_bound_bin_value;
std::vector<colvarvalue> curr_values(num_variables());
for (ic = 0; ic < num_variables(); ic++) {
curr_values[ic].type(variables(ic)->value());
}
std::vector<int> curr_bin;
curr_values = values ? *values : colvar_values;
std::vector<bool> add_force(num_variables());
for (ir = 0; ir < replicas.size(); ir++) {
Expand All @@ -1338,20 +1315,18 @@ int colvarbias_meta::calc_forces(std::vector<colvarvalue> const *values)
}
ii=which_int_ulimit_cv[ic];
if (ii>-1) {
if ( curr_values[ic]>=interval_ulimit[ii] ) {
if ( curr_values[ic]>interval_ulimit[ii] ) {
add_force[ic]=false;
up_bound_bin_value=hills_energy->lower_boundaries[ic].real_value+variables(ic)->width*(0.5+cvm::floor((interval_ulimit[ii]-hills_energy->lower_boundaries[ic].real_value)/variables(ic)->width));
//if (interval_ulimit[ii]==hills_energy->upper_boundaries[ic].real_value){
if (up_bound_bin_value>hills_energy->upper_boundaries[ic].real_value) {
curr_values[ic]=interval_ulimit[ii]-0.5*(variables(ic)->width); // upper border is out of grid; in this way is in
} else {
curr_values[ic]=interval_ulimit[ii];
}
curr_values[ic]=interval_ulimit[ii];
}
}
}

std::vector<int> const curr_bin = hills_energy->get_colvars_index(curr_values);
if (use_interval) {
curr_bin = hills_energy->get_colvars_index_bound(curr_values);
} else {
curr_bin = hills_energy->get_colvars_index(curr_values);
}

if (hills_energy->index_ok(curr_bin)) {
for (ir = 0; ir < replicas.size(); ir++) {
Expand Down Expand Up @@ -1381,25 +1356,6 @@ int colvarbias_meta::calc_forces(std::vector<colvarvalue> const *values)
// now include the hills that have not been binned yet (starting
// from new_hills_begin)

if (use_interval) {
curr_values = values ? *values : colvar_values;
for (ic = 0; ic < num_variables(); ic++) {
ii=which_int_llimit_cv[ic];
if (ii>-1) {
if ( curr_values[ic]<interval_llimit[ii] ) {
curr_values[ic]=interval_llimit[ii];
}
}
ii=which_int_ulimit_cv[ic];
if (ii>-1) {
if ( curr_values[ic]>interval_ulimit[ii] ) {
curr_values[ic]=interval_ulimit[ii];
}
}
}
}


if (cvm::debug()) {
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
Expand Down
3 changes: 3 additions & 0 deletions src/colvarbias_meta.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -221,6 +221,9 @@ class colvarbias_meta
std::vector<cvm::real> interval_llimit;
std::vector<cvm::real> interval_ulimit;

/// \brief Current value of colvars to be modifed for calculation of energy and forces with interval
std::vector<colvarvalue> curr_values;

/// Ensemble-biased metadynamics (EBmeta) flag
bool ebmeta;

Expand Down
11 changes: 11 additions & 0 deletions src/colvargrid.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -625,6 +625,17 @@ template <class T> class colvar_grid : public colvarparse {

/// \brief Get the bin indices corresponding to the provided values of
/// the colvars and assign first or last bin if out of boundaries
inline std::vector<int> const get_colvars_index_bound(std::vector<colvarvalue> const &values) const
{
std::vector<int> index = new_index();
for (size_t i = 0; i < nd; i++) {
index[i] = value_to_bin_scalar_bound(values[i], i);
}
return index;
}

/// \brief Get the bin indices corresponding to the current values of
/// the colvars and assign first or last bin if out of boundaries
inline std::vector<int> const get_colvars_index_bound() const
{
std::vector<int> index = new_index();
Expand Down

0 comments on commit 010d8a4

Please sign in to comment.