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Condense and simplify metadynamics state reading
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@giacomofiorin
giacomofiorin committed Aug 23, 2023
1 parent be6e37f commit eb94ac2
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Showing 2 changed files with 105 additions and 106 deletions.
198 changes: 92 additions & 106 deletions src/colvarbias_meta.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias_meta.h"
#include "colvars_memstream.h"


colvarbias_meta::colvarbias_meta(char const *key)
Expand Down Expand Up @@ -1293,6 +1294,36 @@ int colvarbias_meta::set_state_params(std::string const &state_conf)
}


template <typename IST, typename GT>
IST & colvarbias_meta::read_grid_data_template_(IST& is, std::string const &key,
GT *grid, GT *backup_grid)
{
auto const start_pos = is.tellg();
std::string key_in;
if (is >> key_in) {
if ((key != key_in) || !(grid->read_restart(is))) {
is.clear();
is.seekg(start_pos);
is.setstate(std::ios::failbit);
if (!rebin_grids) {
if ((backup_grid == nullptr) || (comm == single_replica)) {
cvm::error("Error: couldn't read grid data for metadynamics bias \""+
this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
"; if useGrids was off when the state file was written, "
"try enabling rebinGrids now to regenerate the grids.\n", COLVARS_INPUT_ERROR);
}
}
}
} else {
is.clear();
is.seekg(start_pos);
is.setstate(std::ios::failbit);
}
return is;
}


std::istream & colvarbias_meta::read_state_data(std::istream& is)
{
if (use_grids) {
Expand All @@ -1311,95 +1342,26 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
hills_energy_gradients = new colvar_grid_gradient(colvars);
}

std::streampos const hills_energy_pos = is.tellg();
std::string key;
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);
if (!rebin_grids) {
if ((hills_energy_backup == NULL) || (comm == single_replica)) {
cvm::error("Error: couldn't read the 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 {
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;
}
}
}
read_grid_data_template_<std::istream, colvar_grid_scalar>(is, "hills_energy", hills_energy,
hills_energy_backup);

std::streampos 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;
read_grid_data_template_<std::istream, colvar_grid_gradient>(
is, "hills_energy_gradients", hills_energy_gradients, hills_energy_gradients_backup);

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;
}
is.clear();
is.seekg(hills_energy_gradients_pos, std::ios::beg);
is.setstate(std::ios::failbit);
} else {
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);
if (!rebin_grids) {
if ((hills_energy_backup == NULL) || (comm == single_replica)) {
cvm::error("Error: couldn't read the 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 {
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");

cvm::log(" read biasing energy and forces from grids.\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;
}
}

// Save references to the end of the list of existing hills, so that it can
// be cleared if hills are read successfully state
// Save references to the end of the list of existing hills, so that they can
// be cleared if hills are read successfully from the stream
bool const existing_hills = !hills.empty();
size_t const old_hills_size = hills.size();
hill_iter old_hills_end = hills.end();
Expand All @@ -1418,12 +1380,15 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
cvm::to_str((hills.back()).it)+".\n");
}
}

is.clear();

new_hills_begin = hills.end();
cvm::log(" read "+cvm::to_str(hills.size() - old_hills_size)+
" additional explicit hills.\n");
cvm::log(" successfully read "+cvm::to_str(hills.size() - old_hills_size)+
" explicit hills from state.\n");

if (existing_hills) {
// Prune any hills that pre-existed those just read
hills.erase(hills.begin(), old_hills_end);
hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end);
if (cvm::debug()) {
Expand All @@ -1432,6 +1397,41 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
}
}

// If rebinGrids is set, rebin the grids based on the current information
rebin_grids_after_restart();

if (use_grids) {
if (!hills_off_grid.empty()) {
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");
}
}

colvarbias_ti::read_state_data(is);

if (cvm::debug())
cvm::log("colvarbias_meta::read_restart() done\n");

has_data = true;

if (comm == multiple_replicas) {
read_replica_files();
}

return is;
}


cvm::memory_stream &colvarbias_meta::read_state_data(cvm::memory_stream &is)
{
// TODO
return is;
}


void colvarbias_meta::rebin_grids_after_restart()
{
if (rebin_grids) {

// allocate new grids (based on the new boundaries and widths just
Expand Down Expand Up @@ -1478,27 +1478,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
if (!hills.empty())
recount_hills_off_grid(hills.begin(), hills.end(), hills_energy);
}

if (use_grids) {
if (!hills_off_grid.empty()) {
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");
}
}

colvarbias_ti::read_state_data(is);

if (cvm::debug())
cvm::log("colvarbias_meta::read_restart() done\n");

has_data = true;

if (comm != single_replica) {
read_replica_files();
}

return is;
}


Expand Down Expand Up @@ -1778,6 +1757,13 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os)
}


cvm::memory_stream &colvarbias_meta::write_state_data(cvm::memory_stream &os)
{
// TODO
return os;
}


int colvarbias_meta::write_state_to_replicas()
{
int error_code = COLVARS_OK;
Expand Down
13 changes: 13 additions & 0 deletions src/colvarbias_meta.h
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Original file line number Diff line number Diff line change
Expand Up @@ -58,8 +58,21 @@ class colvarbias_meta

virtual std::string const get_state_params() const;
virtual int set_state_params(std::string const &state_conf);

virtual std::ostream &write_state_data(std::ostream &os);
virtual cvm::memory_stream &write_state_data(cvm::memory_stream &os);
virtual std::istream &read_state_data(std::istream &is);
virtual cvm::memory_stream &read_state_data(cvm::memory_stream &is);

private:

template <typename IST, typename GT>
IST &read_grid_data_template_(IST &is, std::string const &key, GT *grid, GT *backup_grid);

public:

/// Function called by read_state_data() to execute rebinning (if requested)
void rebin_grids_after_restart();

virtual int setup_output();
virtual int write_output_files();
Expand Down

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