lammps/lib/colvars/colvarbias_abf.cpp

/// -*- c++ -*-

#include "colvarmodule.h"
#include "colvar.h"
#include "colvarbias_abf.h"

/// ABF bias constructor; parses the config file

colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
  : colvarbias(conf, key),
    gradients(NULL),
    samples(NULL)
{
  // TODO relax this in case of VMD plugin
  if (cvm::temperature() == 0.0)
    cvm::log("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");

  // ************* parsing general ABF options ***********************

  get_keyval(conf, "applyBias",  apply_bias, true);
  if (!apply_bias) cvm::log("WARNING: ABF biases will *not* be applied!\n");

  get_keyval(conf, "updateBias",  update_bias, true);
  if (!update_bias) cvm::log("WARNING: ABF biases will *not* be updated!\n");

  get_keyval(conf, "hideJacobian", hide_Jacobian, false);
  if (hide_Jacobian) {
    cvm::log("Jacobian (geometric) forces will be handled internally.\n");
  } else {
    cvm::log("Jacobian (geometric) forces will be included in reported free energy gradients.\n");
  }

  get_keyval(conf, "fullSamples", full_samples, 200);
  if ( full_samples <= 1 ) full_samples = 1;
  min_samples = full_samples / 2;
  // full_samples - min_samples >= 1 is guaranteed

  get_keyval(conf, "inputPrefix",  input_prefix, std::vector<std::string> ());
  get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
  get_keyval(conf, "historyFreq", history_freq, 0);
  b_history_files = (history_freq > 0);

  // shared ABF
  get_keyval(conf, "shared", shared_on, false);
  if (shared_on) {
    if (!cvm::replica_enabled() || cvm::replica_num() <= 1)
      cvm::error("Error: shared ABF requires more than one replica.");
    else
      cvm::log("shared ABF will be applied among "+ cvm::to_str(cvm::replica_num()) + " replicas.\n");

    // If shared_freq is not set, we default to output_freq
    get_keyval(conf, "sharedFreq", shared_freq, output_freq);
  }

  // ************* checking the associated colvars *******************

  if (colvars.size() == 0) {
    cvm::error("Error: no collective variables specified for the ABF bias.\n");
  }

  if (update_bias) {
  // Request calculation of system force (which also checks for availability)
    enable(f_cvb_get_system_force);
  }
  if (apply_bias) {
    enable(f_cvb_apply_force);
  }

  for (size_t i = 0; i < colvars.size(); i++) {

    if (colvars[i]->value().type() != colvarvalue::type_scalar) {
      cvm::error("Error: ABF bias can only use scalar-type variables.\n");
    }
    colvars[i]->enable(f_cv_grid);
    if (hide_Jacobian) {
      colvars[i]->enable(f_cv_hide_Jacobian);
    }

    // Here we could check for orthogonality of the Cartesian coordinates
    // and make it just a warning if some parameter is set?
  }

  if (get_keyval(conf, "maxForce", max_force)) {
    if (max_force.size() != colvars.size()) {
      cvm::error("Error: Number of parameters to maxForce does not match number of colvars.");
    }
    for (size_t i=0; i<colvars.size(); i++) {
      if (max_force[i] < 0.0) {
        cvm::error("Error: maxForce should be non-negative.");
      }
    }
    cap_force = true;
  } else {
    cap_force = false;
  }

  bin.assign(colvars.size(), 0);
  force_bin.assign(colvars.size(), 0);
  force = new cvm::real [colvars.size()];

  // Construct empty grids based on the colvars
  if (cvm::debug()) {
    cvm::log("Allocating count and free energy gradient grids.\n");
  }

  samples   = new colvar_grid_count(colvars);
  gradients = new colvar_grid_gradient(colvars);
  gradients->samples = samples;
  samples->has_parent_data = true;

  // For shared ABF, we store a second set of grids.
  // This used to be only if "shared" was defined,
  // but now we allow calling share externally (e.g. from Tcl).
  last_samples   = new colvar_grid_count(colvars);
  last_gradients = new colvar_grid_gradient(colvars);
  last_gradients->samples = last_samples;
  last_samples->has_parent_data = true;
  shared_last_step = -1;

  // If custom grids are provided, read them
  if ( input_prefix.size() > 0 ) {
    read_gradients_samples();
  }

  cvm::log("Finished ABF setup.\n");
}

/// Destructor
colvarbias_abf::~colvarbias_abf()
{
  if (samples) {
    delete samples;
    samples = NULL;
  }

  if (gradients) {
    delete gradients;
    gradients = NULL;
  }

  // shared ABF
  // We used to only do this if "shared" was defined,
  // but now we can call shared externally
  if (last_samples) {
    delete last_samples;
    last_samples = NULL;
  }

  if (last_gradients) {
    delete last_gradients;
    last_gradients = NULL;
  }

  delete [] force;

  if (cvm::n_abf_biases > 0)
    cvm::n_abf_biases -= 1;
}


/// Update the FE gradient, compute and apply biasing force
/// also output data to disk if needed

int colvarbias_abf::update()
{
  if (cvm::debug()) cvm::log("Updating ABF bias " + this->name);

  if (cvm::step_relative() == 0) {

    // At first timestep, do only:
    // initialization stuff (file operations relying on n_abf_biases
    // compute current value of colvars

    for (size_t i=0; i<colvars.size(); i++) {
      bin[i] = samples->current_bin_scalar(i);
    }

  } else {

    for (size_t i=0; i<colvars.size(); i++) {
      bin[i] = samples->current_bin_scalar(i);
    }

    if ( update_bias && samples->index_ok(force_bin) ) {
      // Only if requested and within bounds of the grid...

      for (size_t i=0; i<colvars.size(); i++) {	  // get forces(lagging by 1 timestep) from colvars
        force[i] = colvars[i]->system_force();
      }
      gradients->acc_force(force_bin, force);
    }
  }

  // save bin for next timestep
  force_bin = bin;

  // Reset biasing forces from previous timestep
  for (size_t i=0; i<colvars.size(); i++) {
    colvar_forces[i].reset();
  }

  // Compute and apply the new bias, if applicable
  if ( apply_bias && samples->index_ok(bin) ) {

    size_t  count = samples->value(bin);
    cvm::real	fact = 1.0;

    // Factor that ensures smooth introduction of the force
    if ( count < full_samples ) {
      fact = ( count < min_samples) ? 0.0 :
        (cvm::real(count - min_samples)) / (cvm::real(full_samples - min_samples));
    }

    const cvm::real * grad  = &(gradients->value(bin));

    if ( fact != 0.0 ) {
      if ( (colvars.size() == 1) && colvars[0]->periodic_boundaries() ) {
        // Enforce a zero-mean bias on periodic, 1D coordinates
        // in other words: boundary condition is that the biasing potential is periodic
        colvar_forces[0].real_value = fact * (grad[0] / cvm::real(count) - gradients->average());
      } else {
        for (size_t i=0; i<colvars.size(); i++) {
          // subtracting the mean force (opposite of the FE gradient) means adding the gradient
          colvar_forces[i].real_value = fact * grad[i] / cvm::real(count);
        }
      }
      if (cap_force) {
        for (size_t i=0; i<colvars.size(); i++) {
          if ( colvar_forces[i].real_value * colvar_forces[i].real_value > max_force[i] * max_force[i] ) {
            colvar_forces[i].real_value = (colvar_forces[i].real_value > 0 ? max_force[i] : -1.0 * max_force[i]);
          }
        }
      }
    }
  }

  // update the output prefix; TODO: move later to setup_output() function
  if ( cvm::n_abf_biases == 1 && cvm::n_meta_biases == 0 ) {
    // This is the only ABF bias
    output_prefix = cvm::output_prefix;
  } else {
    output_prefix = cvm::output_prefix + "." + this->name;
  }

  if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
    if (cvm::debug()) cvm::log("ABF bias trying to write gradients and samples to disk");
    write_gradients_samples(output_prefix);
  }

  if (b_history_files && (cvm::step_absolute() % history_freq) == 0) {
    cvm::log("ABFHISTORYFILE "+cvm::to_str(cvm::step_absolute()));
    // file already exists iff cvm::step_relative() > 0
    // otherwise, backup and replace
    write_gradients_samples(output_prefix + ".hist", (cvm::step_relative() > 0));
  }

  if (shared_on && shared_last_step >= 0 && cvm::step_absolute() % shared_freq == 0) {
    // Share gradients and samples for shared ABF.
    replica_share();
  }

  // Prepare for the first sharing.
  if (shared_last_step < 0) {
    // Copy the current gradient and count values into last.
    last_gradients->copy_grid(*gradients);
    last_samples->copy_grid(*samples);
    shared_last_step = cvm::step_absolute();
    cvm::log("Prepared sample and gradient buffers at step "+cvm::to_str(cvm::step_absolute())+".");
  }

  return COLVARS_OK;
}

int colvarbias_abf::replica_share() {
  int p;

  if ( !cvm::replica_enabled() ) {
    cvm::error("Error: shared ABF: No replicas.\n");
    return COLVARS_ERROR;
  }
  // We must have stored the last_gradients and last_samples.
  if (shared_last_step < 0 ) {
    cvm::error("Error: shared ABF: Tried to apply shared ABF before any sampling had occurred.\n");
    return COLVARS_ERROR;
  }

  // Share gradients for shared ABF.
  cvm::log("shared ABF: Sharing gradient and samples among replicas at step "+cvm::to_str(cvm::step_absolute()) );

  // Count of data items.
  size_t data_n = gradients->raw_data_num();
  size_t samp_start = data_n*sizeof(cvm::real);
  size_t msg_total = data_n*sizeof(size_t) + samp_start;
  char* msg_data = new char[msg_total];

  if (cvm::replica_index() == 0) {
    // Replica 0 collects the delta gradient and count from the others.
    for (p = 1; p < cvm::replica_num(); p++) {
      // Receive the deltas.
      cvm::replica_comm_recv(msg_data, msg_total, p);

      // Map the deltas from the others into the grids.
      last_gradients->raw_data_in((cvm::real*)(&msg_data[0]));
      last_samples->raw_data_in((size_t*)(&msg_data[samp_start]));

      // Combine the delta gradient and count of the other replicas
      // with Replica 0's current state (including its delta).
      gradients->add_grid( *last_gradients );
      samples->add_grid( *last_samples );
    }

    // Now we must send the combined gradient to the other replicas.
    gradients->raw_data_out((cvm::real*)(&msg_data[0]));
    samples->raw_data_out((size_t*)(&msg_data[samp_start]));
    for (p = 1; p < cvm::replica_num(); p++) {
      cvm::replica_comm_send(msg_data, msg_total, p);
    }

  } else {
    // All other replicas send their delta gradient and count.
    // Calculate the delta gradient and count.
    last_gradients->delta_grid(*gradients);
    last_samples->delta_grid(*samples);

    // Cast the raw char data to the gradient and samples.
    last_gradients->raw_data_out((cvm::real*)(&msg_data[0]));
    last_samples->raw_data_out((size_t*)(&msg_data[samp_start]));
    cvm::replica_comm_send(msg_data, msg_total, 0);

    // We now receive the combined gradient from Replica 0.
    cvm::replica_comm_recv(msg_data, msg_total, 0);
    // We sync to the combined gradient computed by Replica 0.
    gradients->raw_data_in((cvm::real*)(&msg_data[0]));
    samples->raw_data_in((size_t*)(&msg_data[samp_start]));
  }

  // Without a barrier it's possible that one replica starts
  // share 2 when other replicas haven't finished share 1.
  cvm::replica_comm_barrier();
  // Done syncing the replicas.
  delete[] msg_data;

  // Copy the current gradient and count values into last.
  last_gradients->copy_grid(*gradients);
  last_samples->copy_grid(*samples);
  shared_last_step = cvm::step_absolute();

  return COLVARS_OK;
}

void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool append)
{
  std::string  samples_out_name = prefix + ".count";
  std::string  gradients_out_name = prefix + ".grad";
  std::ios::openmode mode = (append ? std::ios::app : std::ios::out);

  cvm::ofstream samples_os;
  cvm::ofstream gradients_os;

  if (!append) cvm::backup_file(samples_out_name.c_str());
  samples_os.open(samples_out_name.c_str(), mode);
  if (!samples_os.is_open()) {
    cvm::error("Error opening ABF samples file " + samples_out_name + " for writing");
  }
  samples->write_multicol(samples_os);
  samples_os.close();

  if (!append) cvm::backup_file(gradients_out_name.c_str());
  gradients_os.open(gradients_out_name.c_str(), mode);
  if (!gradients_os.is_open()) {
    cvm::error("Error opening ABF gradient file " + gradients_out_name + " for writing");
  }
  gradients->write_multicol(gradients_os);
  gradients_os.close();

  if (colvars.size() == 1) {
    std::string  pmf_out_name = prefix + ".pmf";
    if (!append) cvm::backup_file(pmf_out_name.c_str());
    cvm::ofstream pmf_os;
    // Do numerical integration and output a PMF
    pmf_os.open(pmf_out_name.c_str(), mode);
    if (!pmf_os.is_open())	cvm::error("Error opening pmf file " + pmf_out_name + " for writing");
    gradients->write_1D_integral(pmf_os);
    pmf_os << std::endl;
    pmf_os.close();
  }
  return;
}


// For Tcl implementation of selection rules.
/// Give the total number of bins for a given bias.
int colvarbias_abf::bin_num() {
  return samples->number_of_points(0);
}
/// Calculate the bin index for a given bias.
int colvarbias_abf::current_bin() {
  return samples->current_bin_scalar(0);
}
/// Give the count at a given bin index.
int colvarbias_abf::bin_count(int bin_index) {
  if (bin_index < 0 || bin_index >= bin_num()) {
    cvm::error("Error: Tried to get bin count from invalid bin index "+cvm::to_str(bin_index));
    return -1;
  }
  std::vector<int> ix(1,(int)bin_index);
  return samples->value(ix);
}


void colvarbias_abf::read_gradients_samples()
{
  std::string samples_in_name, gradients_in_name;

  for ( size_t i = 0; i < input_prefix.size(); i++ ) {
    samples_in_name = input_prefix[i] + ".count";
    gradients_in_name = input_prefix[i] + ".grad";
    // For user-provided files, the per-bias naming scheme may not apply

    std::ifstream is;

    cvm::log("Reading sample count from " + samples_in_name + " and gradients from " + gradients_in_name);
    is.open(samples_in_name.c_str());
    if (!is.is_open()) cvm::error("Error opening ABF samples file " + samples_in_name + " for reading");
    samples->read_multicol(is, true);
    is.close();
    is.clear();

    is.open(gradients_in_name.c_str());
    if (!is.is_open())	cvm::error("Error opening ABF gradient file " + gradients_in_name + " for reading");
    gradients->read_multicol(is, true);
    is.close();
  }
  return;
}


std::ostream & colvarbias_abf::write_restart(std::ostream& os)
{

  std::ios::fmtflags flags(os.flags());
  os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format

  os << "abf {\n"
     << "  configuration {\n"
     << "    name " << this->name << "\n";
  os << "  }\n";

  os << "samples\n";
  samples->write_raw(os, 8);

  os << "\ngradient\n";
  gradients->write_raw(os);

  os << "}\n\n";

  os.flags(flags);
  return os;
}


std::istream & colvarbias_abf::read_restart(std::istream& is)
{
  if ( input_prefix.size() > 0 ) {
    cvm::error("ERROR: cannot provide both inputPrefix and restart information(colvarsInput)");
  }

  size_t const start_pos = is.tellg();

  cvm::log("Restarting ABF bias \""+
            this->name+"\".\n");
  std::string key, brace, conf;

  if ( !(is >> key)   || !(key == "abf") ||
       !(is >> brace) || !(brace == "{") ||
       !(is >> colvarparse::read_block("configuration", conf)) ) {
    cvm::log("Error: in reading restart configuration for ABF bias \""+
              this->name+"\" at position "+
              cvm::to_str(is.tellg())+" in stream.\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::error("Error: in the restart file, the "
                      "\"abf\" block has wrong name(" + name + ")\n");
  if ( name == "" ) {
    cvm::error("Error: \"abf\" block in the restart file has no name.\n");
  }

  if ( !(is >> key)   || !(key == "samples")) {
    cvm::log("Error: in reading restart configuration for ABF bias \""+
              this->name+"\" at position "+
              cvm::to_str(is.tellg())+" in stream.\n");
    is.clear();
    is.seekg(start_pos, std::ios::beg);
    is.setstate(std::ios::failbit);
    return is;
  }
  if (! samples->read_raw(is)) {
    is.clear();
    is.seekg(start_pos, std::ios::beg);
    is.setstate(std::ios::failbit);
    return is;
  }

  if ( !(is >> key)   || !(key == "gradient")) {
    cvm::log("Error: in reading restart configuration for ABF bias \""+
              this->name+"\" at position "+
              cvm::to_str(is.tellg())+" in stream.\n");
    is.clear();
    is.seekg(start_pos, std::ios::beg);
    is.setstate(std::ios::failbit);
    return is;
  }
  if (! gradients->read_raw(is)) {
    is.clear();
    is.seekg(start_pos, std::ios::beg);
    is.setstate(std::ios::failbit);
    return is;
  }

  is >> brace;
  if (brace != "}") {
    cvm::error("Error: corrupt restart information for ABF bias \""+
                      this->name+"\": no matching brace at position "+
                      cvm::to_str(is.tellg())+" in the restart file.\n");
    is.setstate(std::ios::failbit);
  }
  return is;
}