Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/lib/colvars/colvarbias_meta.cpp
585a65c560felammm-master-deprecated

Last Change
Raw File

colvarbias_meta.cpp
View Options

/// -*- c++ -*-
#include <iostream>
#include <sstream>
#include <fstream>
#include <iomanip>
#include <cmath>
#include <algorithm>
// used to set the absolute path of a replica file
#if defined(WIN32) && !defined(__CYGWIN__)
#include <direct.h>
#define CHDIR ::_chdir
#define GETCWD ::_getcwd
#define PATHSEP "\\"
#else
#include <unistd.h>
#define CHDIR ::chdir
#define GETCWD ::getcwd
#define PATHSEP "/"
#endif
#include "colvar.h"
#include "colvarbias_meta.h"
colvarbias_meta::colvarbias_meta()
: colvarbias(),
new_hills_begin(hills.end()),
state_file_step(0)
{
}
colvarbias_meta::colvarbias_meta(std::string const &conf, char const *key)
: colvarbias(conf, key),
new_hills_begin(hills.end()),
state_file_step(0)
{
if (cvm::n_abf_biases > 0)
cvm::log("Warning: running ABF and metadynamics together is not recommended unless applyBias is off for ABF.\n");
get_keyval(conf, "hillWeight", hill_weight, 0.01);
if (hill_weight == 0.0)
cvm::log("Warning: hillWeight has been set to zero, "
"this bias will have no effect.\n");
get_keyval(conf, "newHillFrequency", new_hill_freq, 1000);
get_keyval(conf, "hillWidth", hill_width, std::sqrt(2.0 * PI) / 2.0);
{
bool b_replicas = false;
get_keyval(conf, "multipleReplicas", b_replicas, false);
if (b_replicas)
comm = multiple_replicas;
else
comm = single_replica;
}
get_keyval(conf, "useGrids", use_grids, true);
if (use_grids) {
get_keyval(conf, "gridsUpdateFrequency", grids_freq, new_hill_freq);
get_keyval(conf, "rebinGrids", rebin_grids, false);
expand_grids = false;
size_t i;
for (i = 0; i < colvars.size(); i++) {
if (colvars[i]->expand_boundaries) {
expand_grids = true;
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": Will expand grids when the colvar \""+
colvars[i]->name+"\" approaches its boundaries.\n");
}
}
get_keyval(conf, "keepHills", keep_hills, false);
if (! get_keyval(conf, "writeFreeEnergyFile", dump_fes, true))
get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false);
for (i = 0; i < colvars.size(); i++) {
colvars[i]->enable(colvar::task_grid);
}
hills_energy = new colvar_grid_scalar(colvars);
hills_energy_gradients = new colvar_grid_gradient(colvars);
} else {
rebin_grids = false;
keep_hills = false;
dump_fes = false;
dump_fes_save = false;
dump_replica_fes = false;
hills_energy = NULL;
hills_energy_gradients = NULL;
}
if (comm != single_replica) {
if (expand_grids)
cvm::fatal_error("Error: expandBoundaries is not supported when "
"using more than one replicas; please allocate "
"wide enough boundaries for each colvar"
"ahead of time.\n");
if (get_keyval(conf, "dumpPartialFreeEnergyFile", dump_replica_fes, false)) {
if (dump_replica_fes && (! dump_fes)) {
cvm::log("Enabling \"dumpFreeEnergyFile\".\n");
}
}
get_keyval(conf, "replicaID", replica_id, std::string(""));
if (!replica_id.size())
cvm::error("Error: replicaID must be defined "
"when using more than one replica.\n", INPUT_ERROR);
get_keyval(conf, "replicasRegistry",
replicas_registry_file,
(this->name+".replicas.registry.txt"));
get_keyval(conf, "replicaUpdateFrequency",
replica_update_freq, new_hill_freq);
if (keep_hills)
cvm::log("Warning: in metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": keepHills with more than one replica can lead to a very "
"large amount of input/output and slow down your calculations. "
"Please consider disabling it.\n");
}
get_keyval(conf, "writeHillsTrajectory", b_hills_traj, false);
// for well-tempered metadynamics
get_keyval(conf, "wellTempered", well_tempered, false);
get_keyval(conf, "biasTemperature", bias_temperature, -1.0);
if ((bias_temperature == -1.0) && well_tempered) {
cvm::fatal_error("Error: biasTemperature is not set.\n");
}
if (well_tempered) {
cvm::log("Well-tempered metadynamics is used.\n");
cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n");
}
if (cvm::debug())
cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
save_delimiters = false;
}
colvarbias_meta::~colvarbias_meta()
{
if (hills_energy) {
delete hills_energy;
hills_energy = NULL;
}
if (hills_energy_gradients) {
delete hills_energy_gradients;
hills_energy_gradients = NULL;
}
if (replica_hills_os.is_open())
replica_hills_os.close();
if (hills_traj_os.is_open())
hills_traj_os.close();
if (cvm::n_meta_biases > 0)
cvm::n_meta_biases -= 1;
}
// **********************************************************************
// Hill management member functions
// **********************************************************************
std::list<colvarbias_meta::hill>::const_iterator
colvarbias_meta::create_hill(colvarbias_meta::hill const &h)
{
hill_iter const hills_end = hills.end();
hills.push_back(h);
if (new_hills_begin == hills_end) {
// if new_hills_begin is unset, set it for the first time
new_hills_begin = hills.end();
new_hills_begin--;
}
if (use_grids) {
// also add it to the list of hills that are off-grid, which may
// need to be computed analytically when the colvar returns
// off-grid
cvm::real const min_dist = hills_energy->bin_distance_from_boundaries(h.centers, true);
if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) {
hills_off_grid.push_back(h);
}
}
// output to trajectory (if specified)
if (hills_traj_os.is_open()) {
hills_traj_os << (hills.back()).output_traj();
if (cvm::debug()) {
hills_traj_os.flush();
}
}
has_data = true;
return hills.end();
}
std::list<colvarbias_meta::hill>::const_iterator
colvarbias_meta::delete_hill(hill_iter &h)
{
if (cvm::debug()) {
cvm::log("Deleting hill from the metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
", with step number "+
cvm::to_str(h->it)+(h->replica.size() ?
", replica id \""+h->replica :
"")+".\n");
}
if (use_grids && !hills_off_grid.empty()) {
for (hill_iter hoff = hills_off_grid.begin();
hoff != hills_off_grid.end(); hoff++) {
if (*h == *hoff) {
hills_off_grid.erase(hoff);
break;
}
}
}
if (hills_traj_os.is_open()) {
// output to the trajectory
hills_traj_os << "# DELETED this hill: "
<< (hills.back()).output_traj()
<< "\n";
if (cvm::debug())
hills_traj_os.flush();
}
return hills.erase(h);
}
cvm::real colvarbias_meta::update()
{
if (cvm::debug())
cvm::log("Updating the metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
if (expand_grids) {
// first of all, expand the grids, if specified
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": current coordinates on the grid: "+
cvm::to_str(curr_bin)+".\n");
bool changed_grids = false;
int const min_buffer =
(3 * (size_t) std::floor(hill_width)) + 1;
std::vector<int> new_sizes(hills_energy->sizes());
std::vector<colvarvalue> new_lower_boundaries(hills_energy->lower_boundaries);
std::vector<colvarvalue> new_upper_boundaries(hills_energy->upper_boundaries);
for (size_t i = 0; i < colvars.size(); i++) {
if (! colvars[i]->expand_boundaries)
continue;
cvm::real &new_lb = new_lower_boundaries[i].real_value;
cvm::real &new_ub = new_upper_boundaries[i].real_value;
int &new_size = new_sizes[i];
bool changed_lb = false, changed_ub = false;
if (!colvars[i]->hard_lower_boundary)
if (curr_bin[i] < min_buffer) {
int const extra_points = (min_buffer - curr_bin[i]);
new_lb -= extra_points * colvars[i]->width;
new_size += extra_points;
// changed offset in this direction => the pointer needs to
// be changed, too
curr_bin[i] += extra_points;
changed_lb = true;
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new lower boundary for colvar \""+
colvars[i]->name+"\", at "+
cvm::to_str(new_lower_boundaries[i])+".\n");
}
if (!colvars[i]->hard_upper_boundary)
if (curr_bin[i] > new_size - min_buffer - 1) {
int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer);
new_ub += extra_points * colvars[i]->width;
new_size += extra_points;
changed_ub = true;
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": new upper boundary for colvar \""+
colvars[i]->name+"\", at "+
cvm::to_str(new_upper_boundaries[i])+".\n");
}
if (changed_lb || changed_ub)
changed_grids = true;
}
if (changed_grids) {
// map everything into new grids
colvar_grid_scalar *new_hills_energy =
new colvar_grid_scalar(*hills_energy);
colvar_grid_gradient *new_hills_energy_gradients =
new colvar_grid_gradient(*hills_energy_gradients);
// supply new boundaries to the new grids
new_hills_energy->lower_boundaries = new_lower_boundaries;
new_hills_energy->upper_boundaries = new_upper_boundaries;
new_hills_energy->setup(new_sizes, 0.0, 1);
new_hills_energy_gradients->lower_boundaries = new_lower_boundaries;
new_hills_energy_gradients->upper_boundaries = new_upper_boundaries;
new_hills_energy_gradients->setup(new_sizes, 0.0, colvars.size());
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;
curr_bin = hills_energy->get_colvars_index();
if (cvm::debug())
cvm::log("Coordinates on the new grid: "+
cvm::to_str(curr_bin)+".\n");
}
}
}
// add a new hill if the required time interval has passed
if ((cvm::step_absolute() % new_hill_freq) == 0) {
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": adding a new hill at step "+cvm::to_str(cvm::step_absolute())+".\n");
switch (comm) {
case single_replica:
if (well_tempered) {
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
}
cvm::real const exp_weight = std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill(hill((hill_weight*exp_weight), colvars, hill_width));
} else {
create_hill(hill(hill_weight, colvars, hill_width));
}
break;
case multiple_replicas:
if (well_tempered) {
cvm::real hills_energy_sum_here = 0.0;
if (use_grids) {
std::vector<int> curr_bin = hills_energy->get_colvars_index();
hills_energy_sum_here = hills_energy->value(curr_bin);
} else {
calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
}
cvm::real const exp_weight = std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill(hill((hill_weight*exp_weight), colvars, hill_width, replica_id));
} else {
create_hill(hill(hill_weight, colvars, hill_width, replica_id));
}
if (replica_hills_os.is_open()) {
replica_hills_os << hills.back();
} else {
cvm::fatal_error("Error: in metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
" while writing hills for the other replicas.\n");
}
break;
}
}
// sync with the other replicas (if needed)
if (comm != single_replica) {
// reread the replicas registry
if ((cvm::step_absolute() % replica_update_freq) == 0) {
update_replicas_registry();
// empty the output buffer
if (replica_hills_os.is_open())
replica_hills_os.flush();
read_replica_files();
}
}
// calculate the biasing energy and forces
bias_energy = 0.0;
for (size_t ir = 0; ir < colvars.size(); ir++) {
colvar_forces[ir].reset();
}
if (comm == multiple_replicas)
for (size_t ir = 0; ir < replicas.size(); ir++) {
replicas[ir]->bias_energy = 0.0;
for (size_t ic = 0; ic < colvars.size(); ic++) {
replicas[ir]->colvar_forces[ic].reset();
}
}
if (use_grids) {
// get the forces from the grid
if ((cvm::step_absolute() % grids_freq) == 0) {
// map the most recent gaussians to the grids
project_hills(new_hills_begin, hills.end(),
hills_energy, hills_energy_gradients);
new_hills_begin = hills.end();
// TODO: we may want to condense all into one replicas array,
// including "this" as the first element
if (comm == multiple_replicas) {
for (size_t ir = 0; ir < replicas.size(); ir++) {
replicas[ir]->project_hills(replicas[ir]->new_hills_begin,
replicas[ir]->hills.end(),
replicas[ir]->hills_energy,
replicas[ir]->hills_energy_gradients);
replicas[ir]->new_hills_begin = replicas[ir]->hills.end();
}
}
}
std::vector<int> curr_bin = hills_energy->get_colvars_index();
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": current coordinates on the grid: "+
cvm::to_str(curr_bin)+".\n");
if (hills_energy->index_ok(curr_bin)) {
// within the grid: add the energy and the forces from there
bias_energy += hills_energy->value(curr_bin);
for (size_t ic = 0; ic < colvars.size(); ic++) {
cvm::real const *f = &(hills_energy_gradients->value(curr_bin));
colvar_forces[ic].real_value += -1.0 * f[ic];
// the gradients are stored, not the forces
}
if (comm == multiple_replicas)
for (size_t ir = 0; ir < replicas.size(); ir++) {
bias_energy += replicas[ir]->hills_energy->value(curr_bin);
cvm::real const *f = &(replicas[ir]->hills_energy_gradients->value(curr_bin));
for (size_t ic = 0; ic < colvars.size(); ic++) {
colvar_forces[ic].real_value += -1.0 * f[ic];
}
}
} else {
// off the grid: compute analytically only the hills at the grid's edges
calc_hills(hills_off_grid.begin(), hills_off_grid.end(), bias_energy);
for (size_t ic = 0; ic < colvars.size(); ic++) {
calc_hills_force(ic, hills_off_grid.begin(), hills_off_grid.end(), colvar_forces);
}
if (comm == multiple_replicas)
for (size_t ir = 0; ir < replicas.size(); ir++) {
calc_hills(replicas[ir]->hills_off_grid.begin(),
replicas[ir]->hills_off_grid.end(),
bias_energy);
for (size_t ic = 0; ic < colvars.size(); ic++) {
calc_hills_force(ic,
replicas[ir]->hills_off_grid.begin(),
replicas[ir]->hills_off_grid.end(),
colvar_forces);
}
}
}
}
// now include the hills that have not been binned yet (starting
// from new_hills_begin)
calc_hills(new_hills_begin, hills.end(), bias_energy);
for (size_t ic = 0; ic < colvars.size(); ic++) {
calc_hills_force(ic, new_hills_begin, hills.end(), colvar_forces);
}
if (cvm::debug())
cvm::log("Hills energy = "+cvm::to_str(bias_energy)+
", hills forces = "+cvm::to_str(colvar_forces)+".\n");
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": adding the forces from the other replicas.\n");
if (comm == multiple_replicas)
for (size_t ir = 0; ir < replicas.size(); ir++) {
calc_hills(replicas[ir]->new_hills_begin,
replicas[ir]->hills.end(),
bias_energy);
for (size_t ic = 0; ic < colvars.size(); ic++) {
calc_hills_force(ic,
replicas[ir]->new_hills_begin,
replicas[ir]->hills.end(),
colvar_forces);
}
if (cvm::debug())
cvm::log("Hills energy = "+cvm::to_str(bias_energy)+
", hills forces = "+cvm::to_str(colvar_forces)+".\n");
}
return bias_energy;
}
void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter h_first,
colvarbias_meta::hill_iter h_last,
cvm::real &energy,
std::vector<colvarvalue> const &colvar_values)
{
std::vector<colvarvalue> curr_values(colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
curr_values[i].type(colvars[i]->value());
}
if (colvar_values.size()) {
for (size_t i = 0; i < colvars.size(); i++) {
curr_values[i] = colvar_values[i];
}
} else {
for (size_t i = 0; i < colvars.size(); i++) {
curr_values[i] = colvars[i]->value();
}
}
for (hill_iter h = h_first; h != h_last; h++) {
// compute the gaussian exponent
cvm::real cv_sqdev = 0.0;
for (size_t i = 0; i < colvars.size(); i++) {
colvarvalue const &x = curr_values[i];
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
cv_sqdev += (colvars[i]->dist2(x, center)) / (half_width*half_width);
}
// compute the gaussian
if (cv_sqdev > 23.0) {
// set it to zero if the exponent is more negative than log(1.0E-05)
h->value(0.0);
} else {
h->value(std::exp(-0.5*cv_sqdev));
}
energy += h->energy();
}
}
void colvarbias_meta::calc_hills_force(size_t const &i,
colvarbias_meta::hill_iter h_first,
colvarbias_meta::hill_iter h_last,
std::vector<colvarvalue> &forces,
std::vector<colvarvalue> const &values)
{
// Retrieve the value of the colvar
colvarvalue const x(values.size() ? values[i] : colvars[i]->value());
// do the type check only once (all colvarvalues in the hills series
// were already saved with their types matching those in the
// colvars)
hill_iter h;
switch (colvars[i]->value().type()) {
case colvarvalue::type_scalar:
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].real_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
(colvars[i]->dist2_lgrad(x, center)).real_value );
}
break;
case colvarvalue::type_3vector:
case colvarvalue::type_unit3vector:
case colvarvalue::type_unit3vectorderiv:
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].rvector_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
(colvars[i]->dist2_lgrad(x, center)).rvector_value );
}
break;
case colvarvalue::type_quaternion:
case colvarvalue::type_quaternionderiv:
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].quaternion_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
(colvars[i]->dist2_lgrad(x, center)).quaternion_value );
}
break;
case colvarvalue::type_vector:
for (h = h_first; h != h_last; h++) {
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].vector1d_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
(colvars[i]->dist2_lgrad(x, center)).vector1d_value );
}
break;
case colvarvalue::type_notset:
case colvarvalue::type_all:
default:
break;
}
}
// **********************************************************************
// grid management functions
// **********************************************************************
void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
colvarbias_meta::hill_iter h_last,
colvar_grid_scalar *he,
colvar_grid_gradient *hg,
bool print_progress)
{
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": projecting hills.\n");
// TODO: improve it by looping over a small subgrid instead of the whole grid
std::vector<colvarvalue> colvar_values(colvars.size());
std::vector<cvm::real> colvar_forces_scalar(colvars.size());
std::vector<int> he_ix = he->new_index();
std::vector<int> hg_ix = (hg != NULL) ? hg->new_index() : std::vector<int> (0);
cvm::real hills_energy_here = 0.0;
std::vector<colvarvalue> hills_forces_here(colvars.size(), 0.0);
size_t count = 0;
size_t const print_frequency = ((hills.size() >= 1000000) ? 1 : (1000000/(hills.size()+1)));
if (hg != NULL) {
// loop over the points of the grid
for ( ;
(he->index_ok(he_ix)) && (hg->index_ok(hg_ix));
count++) {
size_t i;
for (i = 0; i < colvars.size(); i++) {
colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
}
// loop over the hills and increment the energy grid locally
hills_energy_here = 0.0;
calc_hills(h_first, h_last, hills_energy_here, colvar_values);
he->acc_value(he_ix, hills_energy_here);
for (i = 0; i < colvars.size(); i++) {
hills_forces_here[i].reset();
calc_hills_force(i, h_first, h_last, hills_forces_here, colvar_values);
colvar_forces_scalar[i] = hills_forces_here[i].real_value;
}
hg->acc_force(hg_ix, &(colvar_forces_scalar.front()));
he->incr(he_ix);
hg->incr(hg_ix);
if ((count % print_frequency) == 0) {
if (print_progress) {
cvm::real const progress = cvm::real(count) / cvm::real(hg->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());
}
}
}
} else {
// simpler version, with just the energy
for ( ; (he->index_ok(he_ix)); ) {
for (size_t i = 0; i < colvars.size(); i++) {
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, 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());
}
}
}
}
if (print_progress) {
cvm::log("100.00% done.");
}
if (! keep_hills) {
hills.erase(hills.begin(), hills.end());
}
}
void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first,
colvarbias_meta::hill_iter h_last,
colvar_grid_scalar *he)
{
hills_off_grid.clear();
for (hill_iter h = h_first; h != h_last; h++) {
cvm::real const min_dist = hills_energy->bin_distance_from_boundaries(h->centers, true);
if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) {
hills_off_grid.push_back(*h);
}
}
}
// **********************************************************************
// multiple replicas functions
// **********************************************************************
void colvarbias_meta::update_replicas_registry()
{
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
": updating the list of replicas, currently containing "+
cvm::to_str(replicas.size())+" elements.\n");
{
// copy the whole file into a string for convenience
std::string line("");
std::ifstream reg_file(replicas_registry_file.c_str());
if (reg_file.is_open()) {
replicas_registry.clear();
while (colvarparse::getline_nocomments(reg_file, line))
replicas_registry.append(line+"\n");
} else {
cvm::error("Error: failed to open file \""+replicas_registry_file+
"\" for reading.\n", FILE_ERROR);
}
}
// now parse it
std::istringstream reg_is(replicas_registry);
if (reg_is.good()) {
std::string new_replica("");
std::string new_replica_file("");
while ((reg_is >> new_replica) && new_replica.size() &&
(reg_is >> new_replica_file) && new_replica_file.size()) {
if (new_replica == this->replica_id) {
// this is the record for this same replica, skip it
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": skipping this replica's own record: \""+
new_replica+"\", \""+new_replica_file+"\"\n");
new_replica_file.clear();
new_replica.clear();
continue;
}
bool already_loaded = false;
for (size_t ir = 0; ir < replicas.size(); ir++) {
if (new_replica == (replicas[ir])->replica_id) {
// this replica was already added
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": skipping a replica already loaded, \""+
(replicas[ir])->replica_id+"\".\n");
already_loaded = true;
break;
}
}
if (!already_loaded) {
// add this replica to the registry
cvm::log("Metadynamics bias \""+this->name+"\""+
": accessing replica \""+new_replica+"\".\n");
replicas.push_back(new colvarbias_meta());
(replicas.back())->replica_id = new_replica;
(replicas.back())->replica_list_file = new_replica_file;
(replicas.back())->replica_state_file = "";
(replicas.back())->replica_state_file_in_sync = false;
// Note: the following could become a copy constructor?
(replicas.back())->name = this->name;
(replicas.back())->colvars = colvars;
(replicas.back())->use_grids = use_grids;
(replicas.back())->dump_fes = false;
(replicas.back())->expand_grids = false;
(replicas.back())->rebin_grids = false;
(replicas.back())->keep_hills = false;
(replicas.back())->colvar_forces = colvar_forces;
(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);
}
}
}
} else {
cvm::fatal_error("Error: cannot read the replicas registry file \""+
replicas_registry+"\".\n");
}
// now (re)read the list file of each replica
for (size_t ir = 0; ir < replicas.size(); ir++) {
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
": reading the list file for replica \""+
(replicas[ir])->replica_id+"\".\n");
std::ifstream list_is((replicas[ir])->replica_list_file.c_str());
std::string key;
std::string new_state_file, new_hills_file;
if (!(list_is >> key) ||
!(key == std::string("stateFile")) ||
!(list_is >> new_state_file) ||
!(list_is >> key) ||
!(key == std::string("hillsFile")) ||
!(list_is >> new_hills_file)) {
cvm::log("Metadynamics bias \""+this->name+"\""+
": failed to read the file \""+
(replicas[ir])->replica_list_file+"\": will try again after "+
cvm::to_str(replica_update_freq)+" steps.\n");
(replicas[ir])->update_status++;
} else {
(replicas[ir])->update_status = 0;
if (new_state_file != (replicas[ir])->replica_state_file) {
cvm::log("Metadynamics bias \""+this->name+"\""+
": replica \""+(replicas[ir])->replica_id+
"\" has supplied a new state file, \""+new_state_file+
"\".\n");
(replicas[ir])->replica_state_file_in_sync = false;
(replicas[ir])->replica_state_file = new_state_file;
(replicas[ir])->replica_hills_file = new_hills_file;
}
}
}
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\": the list of replicas contains "+
cvm::to_str(replicas.size())+" elements.\n");
}
void colvarbias_meta::read_replica_files()
{
for (size_t ir = 0; ir < replicas.size(); ir++) {
if (! (replicas[ir])->replica_state_file_in_sync) {
// if a new state file is being read, the hills file is also new
(replicas[ir])->replica_hills_file_pos = 0;
}
// (re)read the state file if necessary
if ( (! (replicas[ir])->has_data) ||
(! (replicas[ir])->replica_state_file_in_sync) ) {
cvm::log("Metadynamics bias \""+this->name+"\""+
": reading the state of replica \""+
(replicas[ir])->replica_id+"\" from file \""+
(replicas[ir])->replica_state_file+"\".\n");
std::ifstream is((replicas[ir])->replica_state_file.c_str());
if (! (replicas[ir])->read_restart(is)) {
cvm::log("Reading from file \""+(replicas[ir])->replica_state_file+
"\" failed or incomplete: will try again in "+
cvm::to_str(replica_update_freq)+" steps.\n");
} else {
// state file has been read successfully
(replicas[ir])->replica_state_file_in_sync = true;
(replicas[ir])->update_status = 0;
}
is.close();
}
// now read the hills added after writing the state file
if ((replicas[ir])->replica_hills_file.size()) {
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
": checking for new hills from replica \""+
(replicas[ir])->replica_id+"\" in the file \""+
(replicas[ir])->replica_hills_file+"\".\n");
// read hills from the other replicas' files; for each file, resume
// the position recorded previously
std::ifstream is((replicas[ir])->replica_hills_file.c_str());
if (is.is_open()) {
// try to resume the previous position
is.seekg((replicas[ir])->replica_hills_file_pos, std::ios::beg);
if (!is.is_open()){
// if fail (the file may have been overwritten), reset this
// position
is.clear();
is.seekg(0, std::ios::beg);
// reset the counter
(replicas[ir])->replica_hills_file_pos = 0;
// schedule to reread the state file
(replicas[ir])->replica_state_file_in_sync = false;
// and record the failure
(replicas[ir])->update_status++;
cvm::log("Failed to read the file \""+(replicas[ir])->replica_hills_file+
"\" at the previous position: will try again in "+
cvm::to_str(replica_update_freq)+" steps.\n");
} else {
while ((replicas[ir])->read_hill(is)) {
// if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
": received a hill from replica \""+
(replicas[ir])->replica_id+
"\" at step "+
cvm::to_str(((replicas[ir])->hills.back()).it)+".\n");
}
is.clear();
// store the position for the next read
(replicas[ir])->replica_hills_file_pos = is.tellg();
if (cvm::debug())
cvm::log("Metadynamics bias \""+this->name+"\""+
": stopped reading file \""+(replicas[ir])->replica_hills_file+
"\" at position "+
cvm::to_str((replicas[ir])->replica_hills_file_pos)+".\n");
// test whether this is the end of the file
is.seekg(0, std::ios::end);
if (is.tellg() > (replicas[ir])->replica_hills_file_pos+1) {
(replicas[ir])->update_status++;
} else {
(replicas[ir])->update_status = 0;
}
}
} else {
cvm::log("Failed to read the file \""+(replicas[ir])->replica_hills_file+
"\": will try again in "+
cvm::to_str(replica_update_freq)+" steps.\n");
(replicas[ir])->update_status++;
// cvm::fatal_error ("Error: cannot read from file \""+
// (replicas[ir])->replica_hills_file+"\".\n");
}
is.close();
}
size_t const n_flush = (replica_update_freq/new_hill_freq + 1);
if ((replicas[ir])->update_status > 3*n_flush) {
// TODO: suspend the calculation?
cvm::log("WARNING: in metadynamics bias \""+this->name+"\""+
" failed to read completely the output of replica \""+
(replicas[ir])->replica_id+
"\" after more than "+
cvm::to_str((replicas[ir])->update_status * replica_update_freq)+
" steps. Ensure that it is still running.\n");
}
}
}
// **********************************************************************
// input functions
// **********************************************************************
std::istream & colvarbias_meta::read_restart(std::istream& is)
{
size_t const start_pos = is.tellg();
if (comm == single_replica) {
// if using a multiple replicas scheme, output messages
// are printed before and after calling this function
cvm::log("Restarting metadynamics bias \""+this->name+"\""+
".\n");
}
std::string key, brace, conf;
if ( !(is >> key) || !(key == "metadynamics") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block("configuration", conf)) ) {
if (comm == single_replica)
cvm::log("Error: in reading restart configuration for metadynamics bias \""+
this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
(replica_state_file_in_sync ? ("at position "+
cvm::to_str(start_pos)+
" in the state file") : "")+".\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
std::string name = "";
if ( colvarparse::get_keyval(conf, "name", name,
std::string(""), colvarparse::parse_silent) &&
(name != this->name) )
cvm::fatal_error("Error: in the restart file, the "
"\"metadynamics\" block has a different name: different system?\n");
if (name.size() == 0) {
cvm::fatal_error("Error: \"metadynamics\" block within the restart file "
"has no identifiers.\n");
}
if (comm != single_replica) {
std::string replica = "";
if (colvarparse::get_keyval(conf, "replicaID", replica,
std::string(""), colvarparse::parse_silent) &&
(replica != this->replica_id))
cvm::fatal_error("Error: in the restart file, the "
"\"metadynamics\" block has a different replicaID: different system?\n");
colvarparse::get_keyval(conf, "step", state_file_step,
cvm::step_absolute(), colvarparse::parse_silent);
}
bool grids_from_restart_file = use_grids;
if (use_grids) {
if (expand_grids) {
// the boundaries of the colvars may have been changed; TODO:
// this reallocation is only for backward-compatibility, and may
// be deleted when grid_parameters (i.e. colvargrid's own
// internal reallocation) has kicked in
delete hills_energy;
delete hills_energy_gradients;
hills_energy = new colvar_grid_scalar(colvars);
hills_energy_gradients = new colvar_grid_gradient(colvars);
}
colvar_grid_scalar *hills_energy_backup = NULL;
colvar_grid_gradient *hills_energy_gradients_backup = NULL;
if (has_data) {
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);
}
size_t const hills_energy_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;
}
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);
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 \""+
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 {
if (comm == single_replica)
cvm::log("Error: couldn't read the free energy grid for metadynamics bias \""+
this->name+"\".\n");
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;
}
}
}
size_t 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;
}
is.clear();
is.seekg(hills_energy_gradients_pos, std::ios::beg);
is.setstate(std::ios::failbit);
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);
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 \""+
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 {
if (comm == single_replica)
cvm::log("Error: couldn't read the free energy gradients grid for metadynamics bias \""+
this->name+"\".\n");
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");
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;
}
}
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)
while (read_hill(is)) {
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");
}
if (rebin_grids) {
// allocate new grids (based on the new boundaries and widths just
// 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);
if (!grids_from_restart_file || (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");
project_hills(hills.begin(), hills.end(),
new_hills_energy, new_hills_energy_gradients, true);
cvm::log("rebinning done.\n");
} else {
// otherwise, use the grids in the restart file
cvm::log("Rebinning the energy and forces grids "
"from the grids in the restart file.\n");
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;
// 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);
}
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");
}
}
is >> brace;
if (brace != "}") {
cvm::log("Incomplete restart information for metadynamics bias \""+
this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": no closing brace at position "+
cvm::to_str(is.tellg())+" in the file.\n");
is.setstate(std::ios::failbit);
return 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) {
read_replica_files();
}
return is;
}
std::istream & colvarbias_meta::read_hill(std::istream &is)
{
if (!is) return is; // do nothing if failbit is set
size_t const start_pos = is.tellg();
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;
}
size_t h_it;
get_keyval(data, "step", h_it, 0, parse_silent);
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_silent);
std::vector<colvarvalue> h_centers(colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
h_centers[i].type(colvars[i]->value());
}
{
// it is safer to read colvarvalue objects one at a time;
// TODO: change this it later
std::string centers_input;
key_lookup(data, "centers", centers_input);
std::istringstream centers_is(centers_input);
for (size_t i = 0; i < colvars.size(); i++) {
centers_is >> h_centers[i];
}
}
std::vector<cvm::real> h_widths(colvars.size());
get_keyval(data, "widths", h_widths,
std::vector<cvm::real> (colvars.size(), (std::sqrt(2.0 * PI) / 2.0)),
parse_silent);
std::string h_replica = "";
if (comm != single_replica) {
get_keyval(data, "replicaID", h_replica, replica_id, parse_silent);
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");
}
hill_iter const hills_end = hills.end();
hills.push_back(hill(h_it, h_weight, h_centers, h_widths, h_replica));
if (new_hills_begin == hills_end) {
// if new_hills_begin is unset, set it for the first time
new_hills_begin = hills.end();
new_hills_begin--;
}
if (use_grids) {
// add this also to the list of hills that are off-grid, which will
// be computed analytically
cvm::real const min_dist =
hills_energy->bin_distance_from_boundaries((hills.back()).centers, true);
if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) {
hills_off_grid.push_back(hills.back());
}
}
has_data = true;
return is;
}
// **********************************************************************
// output functions
// **********************************************************************
int colvarbias_meta::setup_output()
{
if (comm == multiple_replicas) {
// TODO: one may want to specify the path manually for intricated filesystems?
char *pwd = new char[3001];
if (GETCWD(pwd, 3000) == NULL)
cvm::fatal_error("Error: cannot get the path of the current working directory.\n");
replica_list_file =
(std::string(pwd)+std::string(PATHSEP)+
this->name+"."+replica_id+".files.txt");
// replica_hills_file and replica_state_file are those written
// by the current replica; within the mirror biases, they are
// those by another replica
replica_hills_file =
(std::string(pwd)+std::string(PATHSEP)+
cvm::output_prefix+".colvars."+this->name+"."+replica_id+".hills");
replica_state_file =
(std::string(pwd)+std::string(PATHSEP)+
cvm::output_prefix+".colvars."+this->name+"."+replica_id+".state");
delete[] pwd;
// now register this replica
// first check that it isn't already there
bool registered_replica = false;
std::ifstream reg_is(replicas_registry_file.c_str());
if (reg_is.is_open()) { // the file may not be there yet
std::string existing_replica("");
std::string existing_replica_file("");
while ((reg_is >> existing_replica) && existing_replica.size() &&
(reg_is >> existing_replica_file) && existing_replica_file.size()) {
if (existing_replica == replica_id) {
// this replica was already registered
replica_list_file = existing_replica_file;
reg_is.close();
registered_replica = true;
break;
}
}
reg_is.close();
}
// if this replica was not included yet, we should generate a
// new record for it: but first, we write this replica's files,
// for the others to read
// open the "hills" buffer file
if (!replica_hills_os.is_open()) {
cvm::backup_file(replica_hills_file.c_str());
replica_hills_os.open(replica_hills_file.c_str());
if (!replica_hills_os.is_open())
cvm::error("Error: in opening file \""+
replica_hills_file+"\" for writing.\n", FILE_ERROR);
replica_hills_os.setf(std::ios::scientific, std::ios::floatfield);
}
// write the state file (so that there is always one available)
write_replica_state_file();
// schedule to read the state files of the other replicas
for (size_t ir = 0; ir < replicas.size(); ir++) {
(replicas[ir])->replica_state_file_in_sync = false;
}
// if we're running without grids, use a growing list of "hills" files
// otherwise, just one state file and one "hills" file as buffer
std::ofstream list_os(replica_list_file.c_str(),
(use_grids ? std::ios::trunc : std::ios::app));
if (! list_os.is_open())
cvm::fatal_error("Error: in opening file \""+
replica_list_file+"\" for writing.\n");
list_os << "stateFile " << replica_state_file << "\n";
list_os << "hillsFile " << replica_hills_file << "\n";
list_os.close();
// finally, if add a new record for this replica to the registry
if (! registered_replica) {
std::ofstream reg_os(replicas_registry_file.c_str(), std::ios::app);
if (! reg_os.is_open())
cvm::error("Error: in opening file \""+
replicas_registry_file+"\" for writing.\n", FILE_ERROR);
reg_os << replica_id << " " << replica_list_file << "\n";
reg_os.close();
}
}
if (b_hills_traj) {
std::string const traj_file_name(cvm::output_prefix+
".colvars."+this->name+
( (comm != single_replica) ?
("."+replica_id) :
("") )+
".hills.traj");
hills_traj_os.open(traj_file_name.c_str());
if (!hills_traj_os.is_open())
cvm::error("Error: in opening hills output file \"" +
traj_file_name+"\".\n", FILE_ERROR);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
std::ostream & colvarbias_meta::write_restart(std::ostream& os)
{
os << "metadynamics {\n"
<< " configuration {\n"
<< " step " << cvm::step_absolute() << "\n"
<< " name " << this->name << "\n";
if (this->comm != single_replica)
os << " replicaID " << this->replica_id << "\n";
os << " }\n\n";
if (use_grids) {
// 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);
new_hills_begin = hills.end();
// write down the grids to the restart file
os << " hills_energy\n";
hills_energy->write_restart(os);
os << " hills_energy_gradients\n";
hills_energy_gradients->write_restart(os);
}
if ( (!use_grids) || keep_hills ) {
// write all hills currently in memory
for (std::list<hill>::const_iterator h = this->hills.begin();
h != this->hills.end();
h++) {
os << *h;
}
} else {
// write just those that are near the grid boundaries
for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
h != this->hills_off_grid.end();
h++) {
os << *h;
}
}
os << "}\n\n";
if (comm != single_replica) {
write_replica_state_file();
// schedule to reread the state files of the other replicas (they
// have also rewritten them)
for (size_t ir = 0; ir < replicas.size(); ir++) {
(replicas[ir])->replica_state_file_in_sync = false;
}
}
if (dump_fes) {
write_pmf();
}
return os;
}
void colvarbias_meta::write_pmf()
{
// allocate a new grid to store the pmf
colvar_grid_scalar *pmf = new colvar_grid_scalar(*hills_energy);
pmf->setup();
std::string fes_file_name_prefix(cvm::output_prefix);
if ((cvm::n_meta_biases > 1) || (cvm::n_abf_biases > 0)) {
// if this is not the only free energy integrator, append
// this bias's name, to distinguish it from the output of the other
// biases producing a .pmf file
// TODO: fix for ABF with updateBias == no
fes_file_name_prefix += ("."+this->name);
}
if ((comm == single_replica) || (dump_replica_fes)) {
// output the PMF from this instance or replica
pmf->reset();
pmf->add_grid(*hills_energy);
cvm::real const max = pmf->maximum_value();
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;
pmf->multiply_constant(well_temper_scale);
}
{
std::string const fes_file_name(fes_file_name_prefix +
((comm != single_replica) ? ".partial" : "") +
(dump_fes_save ?
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
cvm::backup_file(fes_file_name.c_str());
cvm::ofstream fes_os(fes_file_name.c_str());
pmf->write_multicol(fes_os);
fes_os.close();
}
}
if (comm != single_replica) {
// output the combined PMF from all replicas
pmf->reset();
pmf->add_grid(*hills_energy);
for (size_t ir = 0; ir < replicas.size(); ir++) {
pmf->add_grid(*(replicas[ir]->hills_energy));
}
cvm::real const max = pmf->maximum_value();
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;
pmf->multiply_constant(well_temper_scale);
}
std::string const fes_file_name(fes_file_name_prefix +
(dump_fes_save ?
"."+cvm::to_str(cvm::step_absolute()) : "") +
".pmf");
cvm::backup_file(fes_file_name.c_str());
cvm::ofstream fes_os(fes_file_name.c_str());
pmf->write_multicol(fes_os);
fes_os.close();
}
delete pmf;
}
void colvarbias_meta::write_replica_state_file()
{
// write down also the restart for the other replicas: TODO: this
// is duplicated code, that could be cleaned up later
cvm::backup_file(replica_state_file.c_str());
cvm::ofstream rep_state_os(replica_state_file.c_str());
if (!rep_state_os.is_open())
cvm::fatal_error("Error: in opening file \""+
replica_state_file+"\" for writing.\n");
rep_state_os.setf(std::ios::scientific, std::ios::floatfield);
rep_state_os << "\n"
<< "metadynamics {\n"
<< " configuration {\n"
<< " name " << this->name << "\n"
<< " step " << cvm::step_absolute() << "\n";
if (this->comm != single_replica) {
rep_state_os << " replicaID " << this->replica_id << "\n";
}
rep_state_os << " }\n\n";
rep_state_os << " hills_energy\n";
rep_state_os << std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width);
hills_energy->write_restart(rep_state_os);
rep_state_os << " hills_energy_gradients\n";
rep_state_os << std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width);
hills_energy_gradients->write_restart(rep_state_os);
if ( (!use_grids) || keep_hills ) {
// write all hills currently in memory
for (std::list<hill>::const_iterator h = this->hills.begin();
h != this->hills.end();
h++) {
rep_state_os << *h;
}
} else {
// write just those that are near the grid boundaries
for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
h != this->hills_off_grid.end();
h++) {
rep_state_os << *h;
}
}
rep_state_os << "}\n\n";
rep_state_os.close();
// reopen the hills file
replica_hills_os.close();
cvm::backup_file(replica_hills_file.c_str());
replica_hills_os.open(replica_hills_file.c_str());
if (!replica_hills_os.is_open())
cvm::fatal_error("Error: in opening file \""+
replica_hills_file+"\" for writing.\n");
replica_hills_os.setf(std::ios::scientific, std::ios::floatfield);
}
std::string colvarbias_meta::hill::output_traj()
{
std::ostringstream os;
os.setf(std::ios::fixed, std::ios::floatfield);
os << std::setw(cvm::it_width) << it << " ";
os.setf(std::ios::scientific, std::ios::floatfield);
size_t i;
os << " ";
for (i = 0; i < centers.size(); i++) {
os << " ";
os << std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width) << centers[i];
}
os << " ";
for (i = 0; i < widths.size(); i++) {
os << " ";
os << std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width) << widths[i];
}
os << " ";
os << std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << W << "\n";
return os.str();
}
std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
{
os.setf(std::ios::scientific, std::ios::floatfield);
os << "hill {\n";
os << " step " << std::setw(cvm::it_width) << h.it << "\n";
os << " weight "
<< std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width)
<< h.W << "\n";
if (h.replica.size())
os << " replicaID " << h.replica << "\n";
size_t i;
os << " centers ";
for (i = 0; i < (h.centers).size(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< h.centers[i];
}
os << "\n";
os << " widths ";
for (i = 0; i < (h.widths).size(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< h.widths[i];
}
os << "\n";
os << "}\n";
return os;
}
c4science · Help