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Update Colvars to version 2021-08-03

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This commit is contained in:
Giacomo Fiorin
2021-08-03 18:03:09 -04:00
parent 50e8d7c36b
commit 2a9be42758
48 changed files with 2557 additions and 527 deletions
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199
lib/colvars/colvarbias_meta.cpp
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@ -50,6 +50,7 @@ colvarbias_meta::colvarbias_meta(char const *key)
dump_fes = true;
keep_hills = false;
restart_keep_hills = false;
dump_fes_save = false;
dump_replica_fes = false;
@ -902,7 +903,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
count++) {
size_t i;
for (i = 0; i < num_variables(); i++) {
new_colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
new_colvar_values[i] = he->bin_to_value_scalar(he_ix[i], i);
}
// loop over the hills and increment the energy grid locally
@ -934,40 +935,12 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
}
} else {
// TODO delete this (never used)
// simpler version, with just the energy
for ( ; (he->index_ok(he_ix)); ) {
for (size_t i = 0; i < num_variables(); i++) {
new_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, &new_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());
}
}
}
cvm::error("No grid object provided in metadynamics::project_hills()\n",
BUG_ERROR);
}
if (print_progress) {
cvm::log("100.00% done.");
cvm::log("100.00% done.\n");
}
if (! keep_hills) {
@ -1281,9 +1254,25 @@ int colvarbias_meta::set_state_params(std::string const &state_conf)
return error_code;
}
colvarparse::get_keyval(state_conf, "keepHills", restart_keep_hills, false,
colvarparse::parse_restart);
if ((!restart_keep_hills) && (cvm::main()->restart_version_number() < 20210604)) {
if (keep_hills) {
cvm::log("Warning: could not ensure that keepHills was enabled when "
"this state file was written; because it is enabled now, "
"it is assumed that it was also then, but please verify.\n");
restart_keep_hills = true;
}
} else {
if (restart_keep_hills) {
cvm::log("This state file/stream contains explicit hills.\n");
}
}
std::string check_replica = "";
if (colvarparse::get_keyval(state_conf, "replicaID", check_replica,
std::string(""), colvarparse::parse_silent) &&
std::string(""), colvarparse::parse_restart) &&
(check_replica != this->replica_id)) {
return cvm::error("Error: in the state file , the "
"\"metadynamics\" block has a different replicaID ("+
@ -1297,8 +1286,6 @@ int colvarbias_meta::set_state_params(std::string const &state_conf)
std::istream & colvarbias_meta::read_state_data(std::istream& is)
{
bool grids_from_restart_file = use_grids;
if (use_grids) {
if (expand_grids) {
@ -1343,7 +1330,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
!(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 \""+
@ -1381,7 +1367,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
!(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 \""+
@ -1419,28 +1404,29 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
}
}
// Save references to the end of the list of existing hills, so that it can
// be cleared if hills are read successfully state
bool const existing_hills = !hills.empty();
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)
// Read any hills following the grid data (if any)
while (read_hill(is)) {
if (cvm::debug())
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.empty())
cvm::log("Read "+cvm::to_str(hills.size())+" hills.\n");
cvm::log("Read "+cvm::to_str(hills.size() - old_hills_size)+" hills.\n");
if (existing_hills) {
hills.erase(hills.begin(), old_hills_end);
hills_off_grid.erase(hills_off_grid.begin(), old_hills_off_grid_end);
}
if (rebin_grids) {
@ -1454,7 +1440,16 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
colvar_grid_gradient *new_hills_energy_gradients =
new colvar_grid_gradient(colvars);
if (!grids_from_restart_file || (keep_hills && !hills.empty())) {
if (cvm::debug()) {
std::ostringstream tmp_os;
tmp_os << "hills_energy parameters:\n";
hills_energy->write_params(tmp_os);
tmp_os << "new_hills_energy parameters:\n";
new_hills_energy->write_params(tmp_os);
cvm::log(tmp_os.str());
}
if (restart_keep_hills && !hills.empty()) {
// 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");
@ -1494,11 +1489,6 @@ std::istream & colvarbias_meta::read_state_data(std::istream& 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) {
@ -1509,6 +1499,15 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
}
inline std::istream & reset_istream(std::istream &is, size_t start_pos)
{
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
std::istream & colvarbias_meta::read_hill(std::istream &is)
{
if (!is) return is; // do nothing if failbit is set
@ -1518,45 +1517,72 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
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;
return reset_istream(is, start_pos);
}
std::istringstream data_is(data);
cvm::step_number h_it = 0L;
get_keyval(data, "step", h_it, h_it, parse_restart);
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_restart);
std::vector<colvarvalue> h_centers(num_variables());
for (i = 0; i < num_variables(); i++) {
h_centers[i].type(variables(i)->value());
}
get_keyval(data, "centers", h_centers, h_centers, parse_restart);
std::vector<cvm::real> h_sigmas(num_variables());
get_keyval(data, "widths", h_sigmas, h_sigmas, parse_restart);
for (i = 0; i < num_variables(); i++) {
// For backward compatibility, read the widths instead of the sigmas
h_sigmas[i] /= 2.0;
}
std::string h_replica;
std::string h_replica = "";
if (comm != single_replica) {
get_keyval(data, "replicaID", h_replica, replica_id, parse_restart);
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");
std::string keyword;
while (data_is >> keyword) {
if (keyword == "step") {
if ( !(data_is >> h_it)) {
return reset_istream(is, start_pos);
}
if ((h_it <= state_file_step) && !restart_keep_hills) {
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;
}
}
if (keyword == "weight") {
if ( !(data_is >> h_weight)) {
return reset_istream(is, start_pos);
}
}
if (keyword == "centers") {
for (i = 0; i < num_variables(); i++) {
if ( !(data_is >> h_centers[i])) {
return reset_istream(is, start_pos);
}
}
}
if (keyword == "widths") {
for (i = 0; i < num_variables(); i++) {
if ( !(data_is >> h_sigmas[i])) {
return reset_istream(is, start_pos);
}
// For backward compatibility, read the widths instead of the sigmas
h_sigmas[i] /= 2.0;
}
}
if (comm != single_replica) {
if (keyword == "replicaID") {
if ( !(data_is >> h_replica)) {
return reset_istream(is, start_pos);
}
if (h_replica != replica_id) {
cvm::error("Error: trying to read a hill created by replica \""+
h_replica+"\" for replica \""+replica_id+
"\"; did you swap output files?\n", INPUT_ERROR);
}
}
}
}
hill_iter const hills_end = hills.end();
@ -1699,8 +1725,12 @@ std::string const colvarbias_meta::hills_traj_file_name() const
std::string const colvarbias_meta::get_state_params() const
{
std::ostringstream os;
if (this->comm != single_replica)
if (keep_hills) {
os << "keepHills on" << "\n";
}
if (this->comm != single_replica) {
os << "replicaID " << this->replica_id << "\n";
}
return (colvarbias::get_state_params() + os.str());
}
@ -1944,6 +1974,7 @@ colvarbias_meta::hill::hill(cvm::step_number it_in,
sigmas(cv_values.size()),
replica(replica_in)
{
hill_value = 0.0;
for (size_t i = 0; i < cv_values.size(); i++) {
centers[i].type(cv_values[i]);
centers[i] = cv_values[i];
@ -1967,7 +1998,9 @@ colvarbias_meta::hill::hill(colvarbias_meta::hill const &h)
centers(h.centers),
sigmas(h.sigmas),
replica(h.replica)
{}
{
hill_value = 0.0;
}
colvarbias_meta::hill::~hill()