// -*- c++ -*-

// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.

#include <sstream>
#include <cstring>

#include "colvarmodule.h"
#include "colvarparse.h"
#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias.h"
#include "colvarbias_abf.h"
#include "colvarbias_alb.h"
#include "colvarbias_histogram.h"
#include "colvarbias_meta.h"
#include "colvarbias_restraint.h"
#include "colvarscript.h"
#include "colvaratoms.h"
#include "colvarcomp.h"


colvarmodule::colvarmodule(colvarproxy *proxy_in)
{
  depth_s = 0;
  log_level_ = 10;

  cv_traj_os = NULL;

  if (proxy == NULL) {
    proxy = proxy_in; // Pointer to the proxy object
    parse = new colvarparse(); // Parsing object for global options
    version_int = proxy->get_version_from_string(COLVARS_VERSION);
  } else {
    // TODO relax this error to handle multiple molecules in VMD
    // once the module is not static anymore
    cvm::error("Error: trying to allocate the collective "
               "variable module twice.\n", BUG_ERROR);
    return;
  }

  cvm::log(cvm::line_marker);
  cvm::log("Initializing the collective variables module, version "+
           cvm::to_str(COLVARS_VERSION)+".\n");
  cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n "
           "http://dx.doi.org/10.1080/00268976.2013.813594\n"
           "in any publication based on this calculation.\n");

  if (proxy->smp_enabled() == COLVARS_OK) {
    cvm::log("SMP parallelism is available.\n");
  }

  // set initial default values

  // "it_restart" will be set by the input state file, if any;
  // "it" should be updated by the proxy
  colvarmodule::it = colvarmodule::it_restart = 0;

  use_scripted_forces = false;
  scripting_after_biases = false;

  colvarmodule::debug_gradients_step_size = 1.0e-07;

  colvarmodule::rotation::monitor_crossings = false;
  colvarmodule::rotation::crossing_threshold = 1.0e-02;

  cv_traj_freq = 100;
  restart_out_freq = proxy->restart_frequency();

  // by default overwrite the existing trajectory file
  cv_traj_append = false;

  cv_traj_write_labels = true;
}


colvarmodule * colvarmodule::main()
{
  return proxy->colvars;
}


std::vector<colvar *> *colvarmodule::variables()
{
  return &colvars;
}


std::vector<colvar *> *colvarmodule::variables_active()
{
  return &colvars_active;
}


std::vector<colvar *> *colvarmodule::variables_active_smp()
{
  return &colvars_smp;
}


std::vector<int> *colvarmodule::variables_active_smp_items()
{
  return &colvars_smp_items;
}


std::vector<colvarbias *> *colvarmodule::biases_active()
{
  return &(biases_active_);
}


size_t colvarmodule::size() const
{
  return colvars.size() + biases.size();
}


int colvarmodule::read_config_file(char const  *config_filename)
{
  cvm::log(cvm::line_marker);
  cvm::log("Reading new configuration from file \""+
           std::string(config_filename)+"\":\n");

  // open the configfile
  config_s.open(config_filename);
  if (!config_s.is_open()) {
    cvm::error("Error: in opening configuration file \""+
               std::string(config_filename)+"\".\n",
               FILE_ERROR);
    return COLVARS_ERROR;
  }

  // read the config file into a string
  std::string conf = "";
  std::string line;
  while (parse->read_config_line(config_s, line)) {
    // Delete lines that contain only white space after removing comments
    if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
      conf.append(line+"\n");
  }
  config_s.close();

  return parse_config(conf);
}


int colvarmodule::read_config_string(std::string const &config_str)
{
  cvm::log(cvm::line_marker);
  cvm::log("Reading new configuration:\n");
  std::istringstream new_config_s(config_str);

  // strip the comments away
  std::string conf = "";
  std::string line;
  while (parse->read_config_line(new_config_s, line)) {
    // Delete lines that contain only white space after removing comments
    if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
      conf.append(line+"\n");
  }

  return parse_config(conf);
}


std::istream & colvarmodule::getline(std::istream &is, std::string &line)
{
  std::string l;
  if (std::getline(is, l)) {
    size_t const sz = l.size();
    if (sz > 0) {
      if (l[sz-1] == '\r' ) {
        line = l.substr(0, sz-1);
      } else {
        line = l;
      }
    } else {
      line.clear();
    }
  }
  return is;
}


int colvarmodule::parse_config(std::string &conf)
{
  extra_conf.clear();

  // Check that the input has matching braces
  if (colvarparse::check_braces(conf, 0) != COLVARS_OK) {
    return cvm::error("Error: unmatched curly braces in configuration.\n",
                      INPUT_ERROR);
  }

  // Parse global options
  if (catch_input_errors(parse_global_params(conf))) {
    return get_error();
  }

  // Parse the options for collective variables
  if (catch_input_errors(parse_colvars(conf))) {
    return get_error();
  }

  // Parse the options for biases
  if (catch_input_errors(parse_biases(conf))) {
    return get_error();
  }

  // Done parsing known keywords, check that all keywords found were valid ones
  if (catch_input_errors(parse->check_keywords(conf, "colvarmodule"))) {
    return get_error();
  }

  // Parse auto-generated configuration (e.g. for back-compatibility)
  if (extra_conf.size()) {
    catch_input_errors(parse_global_params(extra_conf));
    catch_input_errors(parse_colvars(extra_conf));
    catch_input_errors(parse_biases(extra_conf));
    parse->check_keywords(extra_conf, "colvarmodule");
    extra_conf.clear();
    if (get_error() != COLVARS_OK) return get_error();
  }

  cvm::log(cvm::line_marker);
  cvm::log("Collective variables module (re)initialized.\n");
  cvm::log(cvm::line_marker);

  // Update any necessary proxy data
  proxy->setup();

  // configuration might have changed, better redo the labels
  cv_traj_write_labels = true;

  return get_error();
}


std::string const & colvarmodule::get_config() const
{
  return parse->get_config();
}


int colvarmodule::append_new_config(std::string const &new_conf)
{
  extra_conf += new_conf;
  return COLVARS_OK;
}


int colvarmodule::parse_global_params(std::string const &conf)
{
  // TODO document and then echo this keyword
  parse->get_keyval(conf, "logLevel", log_level_, log_level_,
                    colvarparse::parse_silent);

  {
    std::string index_file_name;
    size_t pos = 0;
    while (parse->key_lookup(conf, "indexFile", &index_file_name, &pos)) {
      cvm::log("# indexFile = \""+index_file_name+"\"\n");
      read_index_file(index_file_name.c_str());
      index_file_name.clear();
    }
  }

  if (parse->get_keyval(conf, "smp", proxy->b_smp_active, proxy->b_smp_active)) {
    if (proxy->b_smp_active == false) {
      cvm::log("SMP parallelism has been disabled.\n");
    }
  }

  bool b_analysis = true;
  if (parse->get_keyval(conf, "analysis", b_analysis, true,
                        colvarparse::parse_silent)) {
    cvm::log("Warning: keyword \"analysis\" is deprecated: it is now set "
             "to true; individual analyses are performed only if requested.");
  }

  parse->get_keyval(conf, "debugGradientsStepSize", debug_gradients_step_size,
                    debug_gradients_step_size,
                    colvarparse::parse_silent);

  parse->get_keyval(conf, "monitorEigenvalueCrossing",
                    colvarmodule::rotation::monitor_crossings,
                    colvarmodule::rotation::monitor_crossings,
                    colvarparse::parse_silent);
  parse->get_keyval(conf, "eigenvalueCrossingThreshold",
                    colvarmodule::rotation::crossing_threshold,
                    colvarmodule::rotation::crossing_threshold,
                    colvarparse::parse_silent);

  parse->get_keyval(conf, "colvarsTrajFrequency", cv_traj_freq, cv_traj_freq);
  parse->get_keyval(conf, "colvarsRestartFrequency",
                    restart_out_freq, restart_out_freq);

  // Deprecate append flag
  parse->get_keyval(conf, "colvarsTrajAppend",
                    cv_traj_append, cv_traj_append, colvarparse::parse_silent);

  parse->get_keyval(conf, "scriptedColvarForces",
                    use_scripted_forces, use_scripted_forces);

  parse->get_keyval(conf, "scriptingAfterBiases",
                    scripting_after_biases, scripting_after_biases);

  if (use_scripted_forces && !proxy->force_script_defined) {
    return cvm::error("User script for scripted colvar forces not found.",
                      INPUT_ERROR);
  }

  return cvm::get_error();
}


int colvarmodule::parse_colvars(std::string const &conf)
{
  if (cvm::debug())
    cvm::log("Initializing the collective variables.\n");

  std::string colvar_conf = "";
  size_t pos = 0;
  while (parse->key_lookup(conf, "colvar", &colvar_conf, &pos)) {

    if (colvar_conf.size()) {
      cvm::log(cvm::line_marker);
      cvm::increase_depth();
      colvars.push_back(new colvar());
      if (((colvars.back())->init(colvar_conf) != COLVARS_OK) ||
          ((colvars.back())->check_keywords(colvar_conf, "colvar") != COLVARS_OK)) {
        cvm::log("Error while constructing colvar number " +
                 cvm::to_str(colvars.size()) + " : deleting.");
        delete colvars.back();  // the colvar destructor updates the colvars array
        return COLVARS_ERROR;
      }
      cvm::decrease_depth();
    } else {
      cvm::error("Error: \"colvar\" keyword found without any configuration.\n", INPUT_ERROR);
      return COLVARS_ERROR;
    }
    cvm::decrease_depth();
    colvar_conf = "";
  }

  if (!colvars.size()) {
    cvm::log("Warning: no collective variables defined.\n");
  }

  if (colvars.size())
    cvm::log(cvm::line_marker);
  cvm::log("Collective variables initialized, "+
           cvm::to_str(colvars.size())+
           " in total.\n");

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


bool colvarmodule::check_new_bias(std::string &conf, char const *key)
{
  if (cvm::get_error() ||
      (biases.back()->check_keywords(conf, key) != COLVARS_OK)) {
    cvm::log("Error while constructing bias number " +
             cvm::to_str(biases.size()) + " : deleting.\n");
    delete biases.back(); // the bias destructor updates the biases array
    return true;
  }
  return false;
}


template <class bias_type>
int colvarmodule::parse_biases_type(std::string const &conf,
                                    char const *keyword)
{
  std::string bias_conf = "";
  size_t conf_saved_pos = 0;
  while (parse->key_lookup(conf, keyword, &bias_conf, &conf_saved_pos)) {
    if (bias_conf.size()) {
      cvm::log(cvm::line_marker);
      cvm::increase_depth();
      biases.push_back(new bias_type(keyword));
      biases.back()->init(bias_conf);
      if (cvm::check_new_bias(bias_conf, keyword) != COLVARS_OK) {
        return COLVARS_ERROR;
      }
      cvm::decrease_depth();
    } else {
      cvm::error("Error: keyword \""+std::string(keyword)+"\" found without configuration.\n",
                 INPUT_ERROR);
      return COLVARS_ERROR;
    }
    bias_conf = "";
  }
  return COLVARS_OK;
}


int colvarmodule::parse_biases(std::string const &conf)
{
  if (cvm::debug())
    cvm::log("Initializing the collective variables biases.\n");

  /// initialize ABF instances
  parse_biases_type<colvarbias_abf>(conf, "abf");

  /// initialize adaptive linear biases
  parse_biases_type<colvarbias_alb>(conf, "ALB");

  /// initialize harmonic restraints
  parse_biases_type<colvarbias_restraint_harmonic>(conf, "harmonic");

  /// initialize harmonic walls restraints
  parse_biases_type<colvarbias_restraint_harmonic_walls>(conf, "harmonicWalls");

  /// initialize histograms
  parse_biases_type<colvarbias_histogram>(conf, "histogram");

  /// initialize histogram restraints
  parse_biases_type<colvarbias_restraint_histogram>(conf, "histogramRestraint");

  /// initialize linear restraints
  parse_biases_type<colvarbias_restraint_linear>(conf, "linear");

  /// initialize metadynamics instances
  parse_biases_type<colvarbias_meta>(conf, "metadynamics");

  if (use_scripted_forces) {
    cvm::log(cvm::line_marker);
    cvm::increase_depth();
    cvm::log("User forces script will be run at each bias update.");
    cvm::decrease_depth();
  }

  std::vector<std::string> const time_biases = time_dependent_biases();
  if (time_biases.size() > 1) {
    cvm::log("WARNING: there are "+cvm::to_str(time_biases.size())+
             " time-dependent biases with non-zero force parameters:\n"+
             cvm::to_str(time_biases)+"\n"+
             "Please ensure that their forces do not counteract each other.\n");
  }

  if (num_biases() || use_scripted_forces) {
    cvm::log(cvm::line_marker);
    cvm::log("Collective variables biases initialized, "+
             cvm::to_str(num_biases())+" in total.\n");
  } else {
    if (!use_scripted_forces) {
      cvm::log("No collective variables biases were defined.\n");
    }
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


size_t colvarmodule::num_variables() const
{
  return colvars.size();
}


size_t colvarmodule::num_variables_feature(int feature_id) const
{
  size_t n = 0;
  for (std::vector<colvar *>::const_iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
    if ((*cvi)->is_enabled(feature_id)) {
      n++;
    }
  }
  return n;
}


size_t colvarmodule::num_biases() const
{
  return biases.size();
}


size_t colvarmodule::num_biases_feature(int feature_id) const
{
  size_t n = 0;
  for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    if ((*bi)->is_enabled(feature_id)) {
      n++;
    }
  }
  return n;
}


size_t colvarmodule::num_biases_type(std::string const &type) const
{
  size_t n = 0;
  for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    if ((*bi)->bias_type == type) {
      n++;
    }
  }
  return n;
}


std::vector<std::string> const colvarmodule::time_dependent_biases() const
{
  size_t i;
  std::vector<std::string> biases_names;
  for (i = 0; i < num_biases(); i++) {
    if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
        biases[i]->is_enabled(colvardeps::f_cvb_active) &&
        (biases[i]->is_enabled(colvardeps::f_cvb_history_dependent) ||
         biases[i]->is_enabled(colvardeps::f_cvb_time_dependent))) {
      biases_names.push_back(biases[i]->name);
    }
  }
  return biases_names;
}


int colvarmodule::catch_input_errors(int result)
{
  if (result != COLVARS_OK || get_error()) {
    set_error_bits(result);
    set_error_bits(INPUT_ERROR);
    parse->init();
    return get_error();
  }
  return COLVARS_OK;
}


colvarbias * colvarmodule::bias_by_name(std::string const &name)
{
  colvarmodule *cv = cvm::main();
  for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
       bi != cv->biases.end();
       bi++) {
    if ((*bi)->name == name) {
      return (*bi);
    }
  }
  return NULL;
}


colvar *colvarmodule::colvar_by_name(std::string const &name)
{
  colvarmodule *cv = cvm::main();
  for (std::vector<colvar *>::iterator cvi = cv->colvars.begin();
       cvi != cv->colvars.end();
       cvi++) {
    if ((*cvi)->name == name) {
      return (*cvi);
    }
  }
  return NULL;
}


cvm::atom_group *colvarmodule::atom_group_by_name(std::string const &name)
{
  colvarmodule *cv = cvm::main();
  for (std::vector<cvm::atom_group *>::iterator agi = cv->named_atom_groups.begin();
       agi != cv->named_atom_groups.end();
       agi++) {
    if ((*agi)->name == name) {
      return (*agi);
    }
  }
  return NULL;
}


void colvarmodule::register_named_atom_group(atom_group *ag) {
  named_atom_groups.push_back(ag);
}


void colvarmodule::unregister_named_atom_group(cvm::atom_group *ag)
{
  for (std::vector<cvm::atom_group *>::iterator agi = named_atom_groups.begin();
       agi != named_atom_groups.end();
       agi++) {
    if (*agi == ag) {
      named_atom_groups.erase(agi);
      break;
    }
  }
}


int colvarmodule::change_configuration(std::string const &bias_name,
                                       std::string const &conf)
{
  // This is deprecated; supported strategy is to delete the bias
  // and parse the new config
  cvm::increase_depth();
  colvarbias *b;
  b = bias_by_name(bias_name);
  if (b == NULL) {
    cvm::error("Error: bias not found: " + bias_name);
    return COLVARS_ERROR;
  }
  b->change_configuration(conf);
  cvm::decrease_depth();
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


std::string colvarmodule::read_colvar(std::string const &name)
{
  cvm::increase_depth();
  colvar *c;
  std::stringstream ss;
  c = colvar_by_name(name);
  if (c == NULL) {
    cvm::error("Error: colvar not found: " + name);
    return std::string();
  }
  ss << c->value();
  cvm::decrease_depth();
  return ss.str();
}

cvm::real colvarmodule::energy_difference(std::string const &bias_name,
                                          std::string const &conf)
{
  cvm::increase_depth();
  colvarbias *b;
  cvm::real energy_diff = 0.;
  b = bias_by_name(bias_name);
  if (b == NULL) {
    cvm::error("Error: bias not found: " + bias_name);
    return 0.;
  }
  energy_diff = b->energy_difference(conf);
  cvm::decrease_depth();
  return energy_diff;
}

int colvarmodule::bias_current_bin(std::string const &bias_name)
{
  cvm::increase_depth();
  int ret;
  colvarbias *b = bias_by_name(bias_name);

  if (b != NULL) {
    ret = b->current_bin();
  } else {
    cvm::error("Error: bias not found.\n");
    ret = COLVARS_ERROR;
  }

  cvm::decrease_depth();
  return ret;
}

int colvarmodule::bias_bin_num(std::string const &bias_name)
{
  cvm::increase_depth();
  int ret;
  colvarbias *b = bias_by_name(bias_name);

  if (b != NULL) {
    ret = b->bin_num();
  } else {
    cvm::error("Error: bias not found.\n");
    ret = COLVARS_ERROR;
  }

  cvm::decrease_depth();
  return ret;
}

int colvarmodule::bias_bin_count(std::string const &bias_name, size_t bin_index)
{
  cvm::increase_depth();
  int ret;
  colvarbias *b = bias_by_name(bias_name);

  if (b != NULL) {
    ret = b->bin_count(bin_index);
  } else {
    cvm::error("Error: bias not found.\n");
    ret = COLVARS_ERROR;
  }

  cvm::decrease_depth();
  return ret;
}

int colvarmodule::bias_share(std::string const &bias_name)
{
  cvm::increase_depth();
  int ret;
  colvarbias *b = bias_by_name(bias_name);

  if (b != NULL) {
    b->replica_share();
    ret = COLVARS_OK;
  } else {
    cvm::error("Error: bias not found.\n");
    ret = COLVARS_ERROR;
  }

  cvm::decrease_depth();
  return ret;
}


int colvarmodule::calc()
{
  int error_code = COLVARS_OK;

  if (cvm::debug()) {
    cvm::log(cvm::line_marker);
    cvm::log("Collective variables module, step no. "+
             cvm::to_str(cvm::step_absolute())+"\n");
  }

  error_code |= calc_colvars();
  // set biasing forces to zero before biases are calculated and summed over
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end(); cvi++) {
    (*cvi)->reset_bias_force();
  }
  error_code |= calc_biases();
  error_code |= update_colvar_forces();

  error_code |= analyze();

  // write trajectory files, if needed
  if (cv_traj_freq && cv_traj_name.size()) {
    error_code |= write_traj_files();
  }

  // write restart files, if needed
  if (restart_out_freq && (cvm::step_relative() > 0) &&
      ((cvm::step_absolute() % restart_out_freq) == 0) ) {
    if (restart_out_name.size()) {
      // Write restart file, if different from main output
      error_code |= write_restart_file(restart_out_name);
    } else {
      error_code |= write_restart_file(output_prefix()+".colvars.state");
    }
    write_output_files();
  }

  error_code |= end_of_step();

  return error_code;
}


int colvarmodule::calc_colvars()
{
  if (cvm::debug())
    cvm::log("Calculating collective variables.\n");
  // calculate collective variables and their gradients

  // First, we need to decide which biases are awake
  // so they can activate colvars as needed
  std::vector<colvarbias *>::iterator bi;
  for (bi = biases.begin(); bi != biases.end(); bi++) {
    int tsf = (*bi)->get_time_step_factor();
    if (tsf > 0 && (step_absolute() % tsf == 0)) {
      (*bi)->enable(colvardeps::f_cvb_awake);
    } else {
      (*bi)->disable(colvardeps::f_cvb_awake);
    }
  }

  int error_code = COLVARS_OK;
  std::vector<colvar *>::iterator cvi;

  // Determine which colvars are active at this iteration
  variables_active()->clear();
  variables_active()->reserve(variables()->size());
  for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
    // Wake up or put to sleep variables
    int tsf = (*cvi)->get_time_step_factor();
    if (tsf > 0 && (step_absolute() % tsf == 0)) {
      (*cvi)->enable(colvardeps::f_cv_awake);
    } else {
      (*cvi)->disable(colvardeps::f_cv_awake);
    }

    if ((*cvi)->is_enabled()) {
      variables_active()->push_back(*cvi);
    }
  }

  // if SMP support is available, split up the work
  if (proxy->smp_enabled() == COLVARS_OK) {

    // first, calculate how much work (currently, how many active CVCs) each colvar has

    variables_active_smp()->clear();
    variables_active_smp_items()->clear();

    variables_active_smp()->reserve(variables_active()->size());
    variables_active_smp_items()->reserve(variables_active()->size());

    // set up a vector containing all components
    cvm::increase_depth();
    for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {

      error_code |= (*cvi)->update_cvc_flags();

      size_t num_items = (*cvi)->num_active_cvcs();
      variables_active_smp()->reserve(variables_active_smp()->size() + num_items);
      variables_active_smp_items()->reserve(variables_active_smp_items()->size() + num_items);
      for (size_t icvc = 0; icvc < num_items; icvc++) {
        variables_active_smp()->push_back(*cvi);
        variables_active_smp_items()->push_back(icvc);
      }
    }
    cvm::decrease_depth();

    // calculate colvar components in parallel
    error_code |= proxy->smp_colvars_loop();

    cvm::increase_depth();
    for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
      error_code |= (*cvi)->collect_cvc_data();
    }
    cvm::decrease_depth();

  } else {

    // calculate colvars one at a time
    cvm::increase_depth();
    for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
      error_code |= (*cvi)->calc();
      if (cvm::get_error()) {
        return COLVARS_ERROR;
      }
    }
    cvm::decrease_depth();
  }

  error_code |= cvm::get_error();
  return error_code;
}


int colvarmodule::calc_biases()
{
  // update the biases and communicate their forces to the collective
  // variables
  if (cvm::debug() && num_biases())
    cvm::log("Updating collective variable biases.\n");

  std::vector<colvarbias *>::iterator bi;
  int error_code = COLVARS_OK;

  // Total bias energy is reset before calling scripted biases
  total_bias_energy = 0.0;

  // update the list of active biases
  // which may have changed based on f_cvb_awake in calc_colvars()
  biases_active()->clear();
  biases_active()->reserve(biases.size());
  for (bi = biases.begin(); bi != biases.end(); bi++) {
    if ((*bi)->is_enabled()) {
      biases_active()->push_back(*bi);
    }
  }

  // if SMP support is available, split up the work
  if (proxy->smp_enabled() == COLVARS_OK) {

    if (use_scripted_forces && !scripting_after_biases) {
      // calculate biases and scripted forces in parallel
      error_code |= proxy->smp_biases_script_loop();
    } else {
      // calculate biases in parallel
      error_code |= proxy->smp_biases_loop();
    }

  } else {

    if (use_scripted_forces && !scripting_after_biases) {
      error_code |= calc_scripted_forces();
    }

    cvm::increase_depth();
    for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
      error_code |= (*bi)->update();
      if (cvm::get_error()) {
        return error_code;
      }
    }
    cvm::decrease_depth();
  }

  for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
    total_bias_energy += (*bi)->get_energy();
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::update_colvar_forces()
{
  int error_code = COLVARS_OK;

  std::vector<colvar *>::iterator cvi;
  std::vector<colvarbias *>::iterator bi;

  // sum the forces from all biases for each collective variable
  if (cvm::debug() && num_biases())
    cvm::log("Collecting forces from all biases.\n");
  cvm::increase_depth();
  for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
    (*bi)->communicate_forces();
    if (cvm::get_error()) {
      return COLVARS_ERROR;
    }
  }
  cvm::decrease_depth();

  if (use_scripted_forces && scripting_after_biases) {
    error_code |= calc_scripted_forces();
  }

  // Now we have collected energies from both built-in and scripted biases
  if (cvm::debug())
    cvm::log("Adding total bias energy: " + cvm::to_str(total_bias_energy) + "\n");
  proxy->add_energy(total_bias_energy);

  cvm::real total_colvar_energy = 0.0;
  // sum up the forces for each colvar, including wall forces
  // and integrate any internal
  // equation of motion (extended system)
  if (cvm::debug())
    cvm::log("Updating the internal degrees of freedom "
             "of colvars (if they have any).\n");
  cvm::increase_depth();
  for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
    // Inactive colvars will only reset their forces and return 0 energy
    total_colvar_energy += (*cvi)->update_forces_energy();
    if (cvm::get_error()) {
      return COLVARS_ERROR;
    }
  }
  cvm::decrease_depth();
  if (cvm::debug())
    cvm::log("Adding total colvar energy: " + cvm::to_str(total_colvar_energy) + "\n");
  proxy->add_energy(total_colvar_energy);

  // make collective variables communicate their forces to their
  // coupled degrees of freedom (i.e. atoms)
  if (cvm::debug())
    cvm::log("Communicating forces from the colvars to the atoms.\n");
  cvm::increase_depth();
  for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
    if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
      (*cvi)->communicate_forces();
      if (cvm::get_error()) {
        return COLVARS_ERROR;
      }
    }
  }
  cvm::decrease_depth();

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::calc_scripted_forces()
{
  // Run user force script, if provided,
  // potentially adding scripted forces to the colvars
  int res;
  res = proxy->run_force_callback();
  if (res == COLVARS_NOT_IMPLEMENTED) {
    cvm::error("Colvar forces scripts are not implemented.");
    return COLVARS_NOT_IMPLEMENTED;
  }
  if (res != COLVARS_OK) {
    cvm::error("Error running user colvar forces script");
    return COLVARS_ERROR;
  }
  return COLVARS_OK;
}


int colvarmodule::write_restart_file(std::string const &out_name)
{
  cvm::log("Saving collective variables state to \""+out_name+"\".\n");
  proxy->backup_file(out_name);
  std::ostream *restart_out_os = proxy->output_stream(out_name);
  if (!restart_out_os) return cvm::get_error();
  if (!write_restart(*restart_out_os)) {
    return cvm::error("Error: in writing restart file.\n", FILE_ERROR);
  }
  proxy->close_output_stream(out_name);
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::write_traj_files()
{
  if (cv_traj_os == NULL) {
    if (open_traj_file(cv_traj_name) != COLVARS_OK) {
      return cvm::get_error();
    } else {
      cv_traj_write_labels = true;
    }
  }

  // write labels in the traj file every 1000 lines and at first timestep
  if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 ||
      cvm::step_relative() == 0 ||
      cv_traj_write_labels) {
    write_traj_label(*cv_traj_os);
  }
  cv_traj_write_labels = false;

  if ((cvm::step_absolute() % cv_traj_freq) == 0) {
    write_traj(*cv_traj_os);
  }

  if (restart_out_freq && (cv_traj_os != NULL)) {
    // flush the trajectory file if we are at the restart frequency
    if ( (cvm::step_relative() > 0) &&
         ((cvm::step_absolute() % restart_out_freq) == 0) ) {
      cvm::log("Synchronizing (emptying the buffer of) trajectory file \""+
               cv_traj_name+"\".\n");
      proxy->flush_output_stream(cv_traj_os);
    }
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::analyze()
{
  if (cvm::debug()) {
    cvm::log("colvarmodule::analyze(), step = "+cvm::to_str(it)+".\n");
  }

  // perform colvar-specific analysis
  for (std::vector<colvar *>::iterator cvi = variables_active()->begin();
       cvi != variables_active()->end();
       cvi++) {
    cvm::increase_depth();
    (*cvi)->analyze();
    cvm::decrease_depth();
  }

  // perform bias-specific analysis
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    cvm::increase_depth();
    (*bi)->analyze();
    cvm::decrease_depth();
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::end_of_step()
{
  if (cvm::debug()) {
    cvm::log("colvarmodule::end_of_step(), step = "+cvm::to_str(it)+".\n");
  }

  for (std::vector<colvar *>::iterator cvi = variables_active()->begin();
       cvi != variables_active()->end();
       cvi++) {
    cvm::increase_depth();
    (*cvi)->end_of_step();
    cvm::decrease_depth();
  }

  // perform bias-specific analysis
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    cvm::increase_depth();
    (*bi)->end_of_step();
    cvm::decrease_depth();
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::setup()
{
  if (this->size() == 0) return cvm::get_error();
  for (std::vector<colvar *>::iterator cvi = variables()->begin();
       cvi != variables()->end();  cvi++) {
    (*cvi)->setup();
  }
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


colvarmodule::~colvarmodule()
{
  if ((proxy->smp_thread_id() == COLVARS_NOT_IMPLEMENTED) ||
      (proxy->smp_thread_id() == 0)) {

    reset();

    // Delete contents of static arrays
    colvarbias::delete_features();
    colvar::delete_features();
    colvar::cvc::delete_features();
    atom_group::delete_features();

    delete parse;
    parse = NULL;
    proxy = NULL;
  }
}


int colvarmodule::reset()
{
  cvm::log("Resetting the Collective Variables module.\n");

  parse->init();

  // Iterate backwards because we are deleting the elements as we go
  for (std::vector<colvarbias *>::reverse_iterator bi = biases.rbegin();
       bi != biases.rend();
       bi++) {
    delete *bi; // the bias destructor updates the biases array
  }
  biases.clear();
  biases_active_.clear();

  // Iterate backwards because we are deleting the elements as we go
  for (std::vector<colvar *>::reverse_iterator cvi = colvars.rbegin();
       cvi != colvars.rend();
       cvi++) {
    delete *cvi; // the colvar destructor updates the colvars array
  }
  colvars.clear();

  index_groups.clear();
  index_group_names.clear();

  proxy->reset();

  if (cv_traj_os != NULL) {
    // Do not close traj file here, as we might not be done with it yet.
    proxy->flush_output_stream(cv_traj_os);
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int colvarmodule::setup_input()
{
  std::string restart_in_name("");

  // read the restart configuration, if available
  if (proxy->input_prefix().size()) {
    // read the restart file
    restart_in_name = proxy->input_prefix();
    std::ifstream input_is(restart_in_name.c_str());
    if (!input_is.good()) {
      // try by adding the suffix
      input_is.clear();
      restart_in_name = restart_in_name+std::string(".colvars.state");
      input_is.open(restart_in_name.c_str());
    }

    if (!input_is.good()) {
      cvm::error("Error: in opening input file \""+
                 std::string(restart_in_name)+"\".\n",
                 FILE_ERROR);
      return COLVARS_ERROR;
    } else {
      cvm::log(cvm::line_marker);
      cvm::log("Restarting from file \""+restart_in_name+"\".\n");
      read_restart(input_is);
      if (cvm::get_error() != COLVARS_OK) {
        return COLVARS_ERROR;
      } else {
        proxy->input_prefix().clear();
      }
      cvm::log(cvm::line_marker);
    }
  }

  return cvm::get_error();
}


int colvarmodule::setup_output()
{
  int error_code = COLVARS_OK;

  // output state file (restart)
  restart_out_name = proxy->restart_output_prefix().size() ?
    std::string(proxy->restart_output_prefix()+".colvars.state") :
    std::string("");

  if (restart_out_name.size()) {
    cvm::log("The restart output state file will be \""+
             restart_out_name+"\".\n");
  }

  output_prefix() = proxy->output_prefix();
  if (output_prefix().size()) {
    cvm::log("The final output state file will be \""+
             (output_prefix().size() ?
              std::string(output_prefix()+".colvars.state") :
              std::string("colvars.state"))+"\".\n");
    // cvm::log (cvm::line_marker);
  }

  cv_traj_name =
    (output_prefix().size() ?
     std::string(output_prefix()+".colvars.traj") :
     std::string(""));

  if (cv_traj_freq && cv_traj_name.size()) {
    error_code |= open_traj_file(cv_traj_name);
  }

  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    error_code |= (*bi)->setup_output();
  }

  if (error_code != COLVARS_OK || cvm::get_error()) {
    set_error_bits(FILE_ERROR);
  }

  return cvm::get_error();
}


std::istream & colvarmodule::read_restart(std::istream &is)
{
  bool warn_total_forces = false;

  {
    // read global restart information
    std::string restart_conf;
    if (is >> colvarparse::read_block("configuration", restart_conf)) {
      parse->get_keyval(restart_conf, "step",
                        it_restart, static_cast<step_number>(0),
                        colvarparse::parse_restart);
        it = it_restart;
      std::string restart_version;
      parse->get_keyval(restart_conf, "version",
                        restart_version, std::string(""),
                        colvarparse::parse_restart);
      if (restart_version.size() && (restart_version != std::string(COLVARS_VERSION))) {
        cvm::log("This state file was generated with version "+restart_version+"\n");
      }
      if ((restart_version.size() == 0) || (restart_version.compare(std::string(COLVARS_VERSION)) < 0)) {
        // check for total force change
        if (proxy->total_forces_enabled()) {
          warn_total_forces = true;
        }
      }
    }
    is.clear();
    parse->clear_keyword_registry();
  }

  // colvars restart
  cvm::increase_depth();
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
    if ( !((*cvi)->read_restart(is)) ) {
      cvm::error("Error: in reading restart configuration for collective variable \""+
                 (*cvi)->name+"\".\n",
                 INPUT_ERROR);
    }
  }

  // biases restart
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    if (!((*bi)->read_state(is))) {
      cvm::error("Error: in reading restart configuration for bias \""+
                 (*bi)->name+"\".\n",
                 INPUT_ERROR);
    }
  }
  cvm::decrease_depth();

  if (warn_total_forces) {
    cvm::log(cvm::line_marker);
    cvm::log("WARNING:\n");
    std::string const warning("### CHANGES IN THE DEFINITION OF SYSTEM FORCES (NOW TOTAL FORCES)\n\
\n\
Starting from the version 2016-08-10 of the Colvars module, \n\
the role of system forces has been replaced by total forces.\n\
\n\
These include *all* forces acting on a collective variable, whether they\n\
come from the force field potential or from external terms\n\
(e.g. restraints), including forces applied by Colvars itself.\n\
\n\
In NAMD, forces applied by Colvars, IMD, SMD, TMD, symmetry\n\
restraints and tclForces are now all counted in the total force.\n\
\n\
In LAMMPS, forces applied by Colvars itself are now counted in the total\n\
force (all forces from other fixes were being counted already).\n\
\n\
\n\
### WHEN IS THIS CHANGE RELEVANT\n\
\n\
This change affects results *only* when (1) outputSystemForce is\n\
requested or (2) the ABF bias is used.  All other usage cases are\n\
*unaffected* (colvar restraints, metadynamics, etc).\n\
\n\
When system forces are reported (flag: outputSystemForce), their values\n\
in the output may change, but the physical trajectory is never affected.\n\
The physical results of ABF calculations may be affected in some cases.\n\
\n\
\n\
### CHANGES TO ABF CALCULATIONS\n\
\n\
Compared to previous Colvars versions, the ABF method will now attempt\n\
to cancel external forces (for example, boundary walls) and it may be\n\
not possible to resume through a state file a simulation that was\n\
performed with a previous version.\n\
\n\
There are three possible scenarios:\n\
\n\
1. No external forces are applied to the atoms used by ABF: results are\n\
unchanged.\n\
\n\
2. Some of the atoms used by ABF experience external forces, but these\n\
forces are not applied directly to the variables used by ABF\n\
(e.g. another colvar that uses the same atoms, tclForces, etc): in this\n\
case, we recommend beginning a new simulation.\n\
\n\
3. External forces are applied to one or more of the colvars used by\n\
ABF, but no other forces are applied to their atoms: you may use the\n\
subtractAppliedForce keyword inside the corresponding colvars to\n\
continue the previous simulation.\n\n");
    cvm::log(warning);
    cvm::log(cvm::line_marker);

    // update this ahead of time in this special case
    output_prefix() = proxy->input_prefix();
    cvm::log("All output files will now be saved with the prefix \""+output_prefix()+".tmp.*\".\n");
    cvm::log(cvm::line_marker);
    cvm::log("Please review the important warning above. After that, you may rename:\n\
\""+output_prefix()+".tmp.colvars.state\"\n\
to:\n\
\""+ proxy->input_prefix()+".colvars.state\"\n");
    output_prefix() = output_prefix()+".tmp";
    write_restart_file(output_prefix()+".colvars.state");
    cvm::error("Exiting with error until issue is addressed.\n", FATAL_ERROR);
  }

  return is;
}


int colvarmodule::backup_file(char const *filename)
{
  return proxy->backup_file(filename);
}


int colvarmodule::write_output_files()
{
  int error_code = COLVARS_OK;

  cvm::increase_depth();
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
    error_code |= (*cvi)->write_output_files();
  }
  cvm::decrease_depth();

  cvm::increase_depth();
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    error_code |= (*bi)->write_output_files();
    error_code |= (*bi)->write_state_to_replicas();
  }
  cvm::decrease_depth();

  if (cv_traj_os != NULL) {
    // do not close, there may be another run command
    proxy->flush_output_stream(cv_traj_os);
  }

  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}



int colvarmodule::read_traj(char const *traj_filename,
                            long        traj_read_begin,
                            long        traj_read_end)
{
  cvm::log("Opening trajectory file \""+
           std::string(traj_filename)+"\".\n");
  std::ifstream traj_is(traj_filename);

  while (true) {
    while (true) {

      std::string line("");

      do {
        if (!colvarparse::getline_nocomments(traj_is, line)) {
          cvm::log("End of file \""+std::string(traj_filename)+
                   "\" reached, or corrupted file.\n");
          traj_is.close();
          return false;
        }
      } while (line.find_first_not_of(colvarparse::white_space) == std::string::npos);

      std::istringstream is(line);

      if (!(is >> it)) return false;

      if ( (it < traj_read_begin) ) {

        if ((it % 1000) == 0)
          std::cerr << "Skipping trajectory step " << it
                    << "                    \r";

        continue;

      } else {

        if ((it % 1000) == 0)
          std::cerr << "Reading from trajectory, step = " << it
                    << "                    \r";

        if ( (traj_read_end > traj_read_begin) &&
             (it > traj_read_end) ) {
          std::cerr << "\n";
          cvm::error("Reached the end of the trajectory, "
                     "read_end = "+cvm::to_str(traj_read_end)+"\n",
                     FILE_ERROR);
          return COLVARS_ERROR;
        }

        for (std::vector<colvar *>::iterator cvi = colvars.begin();
             cvi != colvars.end();
             cvi++) {
          if (!(*cvi)->read_traj(is)) {
            cvm::error("Error: in reading colvar \""+(*cvi)->name+
                       "\" from trajectory file \""+
                       std::string(traj_filename)+"\".\n",
                       FILE_ERROR);
            return COLVARS_ERROR;
          }
        }

        break;
      }
    }
  }
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


std::ostream & colvarmodule::write_restart(std::ostream &os)
{
  os.setf(std::ios::scientific, std::ios::floatfield);
  os << "configuration {\n"
     << "  step " << std::setw(it_width)
     << it << "\n"
     << "  dt " << dt() << "\n"
     << "  version " << std::string(COLVARS_VERSION) << "\n"
     << "}\n\n";

  int error_code = COLVARS_OK;

  cvm::increase_depth();
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
    (*cvi)->write_restart(os);
  }

  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    (*bi)->write_state(os);
  }
  cvm::decrease_depth();

  if (error_code != COLVARS_OK) {
    // TODO make this function return an int instead
    os.setstate(std::ios::failbit);
  }

  return os;
}


int colvarmodule::open_traj_file(std::string const &file_name)
{
  if (cv_traj_os != NULL) {
    return COLVARS_OK;
  }

  // (re)open trajectory file
  if (cv_traj_append) {
    cvm::log("Appending to colvar trajectory file \""+file_name+
             "\".\n");
    cv_traj_os = (cvm::proxy)->output_stream(file_name, std::ios::app);
  } else {
    cvm::log("Writing to colvar trajectory file \""+file_name+
             "\".\n");
    proxy->backup_file(file_name.c_str());
    cv_traj_os = (cvm::proxy)->output_stream(file_name);
  }

  if (cv_traj_os == NULL) {
    cvm::error("Error: cannot write to file \""+file_name+"\".\n",
               FILE_ERROR);
  }

  return cvm::get_error();
}


int colvarmodule::close_traj_file()
{
  if (cv_traj_os != NULL) {
    proxy->close_output_stream(cv_traj_name);
    cv_traj_os = NULL;
  }
  return cvm::get_error();
}


std::ostream & colvarmodule::write_traj_label(std::ostream &os)
{
  os.setf(std::ios::scientific, std::ios::floatfield);

  os << "# " << cvm::wrap_string("step", cvm::it_width-2)
     << " ";

  cvm::increase_depth();
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
    (*cvi)->write_traj_label(os);
  }
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    (*bi)->write_traj_label(os);
  }
  os << "\n";

  if (cvm::debug()) {
    proxy->flush_output_stream(&os);
  }

  cvm::decrease_depth();
  return os;
}


std::ostream & colvarmodule::write_traj(std::ostream &os)
{
  os.setf(std::ios::scientific, std::ios::floatfield);

  os << std::setw(cvm::it_width) << it
     << " ";

  cvm::increase_depth();
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
    (*cvi)->write_traj(os);
  }
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    (*bi)->write_traj(os);
  }
  os << "\n";

  if (cvm::debug()) {
    proxy->flush_output_stream(&os);
  }

  cvm::decrease_depth();
  return os;
}


void cvm::log(std::string const &message, int min_log_level)
{
  if (cvm::log_level() < min_log_level) return;
  // allow logging when the module is not fully initialized
  size_t const d = (cvm::main() != NULL) ? depth() : 0;
  if (d > 0) {
    proxy->log((std::string(2*d, ' '))+message);
  } else {
    proxy->log(message);
  }
}


void cvm::increase_depth()
{
  (depth())++;
}


void cvm::decrease_depth()
{
  if (depth() > 0) {
    (depth())--;
  }
}


size_t & cvm::depth()
{
  // NOTE: do not call log() or error() here, to avoid recursion
  colvarmodule *cv = cvm::main();
  if (proxy->smp_enabled() == COLVARS_OK) {
    int const nt = proxy->smp_num_threads();
    if (int(cv->depth_v.size()) != nt) {
      proxy->smp_lock();
      // update array of depths
      if (cv->depth_v.size() > 0) { cv->depth_s = cv->depth_v[0]; }
      cv->depth_v.clear();
      cv->depth_v.assign(nt, cv->depth_s);
      proxy->smp_unlock();
    }
    return cv->depth_v[proxy->smp_thread_id()];
  }
  return cv->depth_s;
}


void colvarmodule::set_error_bits(int code)
{
  if (code < 0) {
    cvm::fatal_error("Error: set_error_bits() received negative error code.\n");
    return;
  }
  proxy->smp_lock();
  errorCode |= code | COLVARS_ERROR;
  proxy->smp_unlock();
}

bool colvarmodule::get_error_bit(int code)
{
  return bool(errorCode & code);
}

void colvarmodule::clear_error()
{
  proxy->smp_lock();
  errorCode = COLVARS_OK;
  proxy->smp_unlock();
}


int colvarmodule::error(std::string const &message, int code)
{
  set_error_bits(code);
  proxy->error(message);
  return get_error();
}


int colvarmodule::fatal_error(std::string const &message)
{
  set_error_bits(FATAL_ERROR);
  proxy->fatal_error(message);
  return get_error();
}


int cvm::read_index_file(char const *filename)
{
  std::ifstream is(filename, std::ios::binary);
  if (!is.good()) {
    cvm::error("Error: in opening index file \""+
               std::string(filename)+"\".\n",
               FILE_ERROR);
  }

  while (is.good()) {
    char open, close;
    std::string group_name;
    if ( (is >> open) && (open == '[') &&
         (is >> group_name) &&
         (is >> close) && (close == ']') ) {
      for (std::list<std::string>::iterator names_i = index_group_names.begin();
           names_i != index_group_names.end();
           names_i++) {
        if (*names_i == group_name) {
          cvm::error("Error: the group name \""+group_name+
                     "\" appears in multiple index files.\n",
                     FILE_ERROR);
        }
      }
      index_group_names.push_back(group_name);
      index_groups.push_back(std::vector<int>());
    } else {
      cvm::error("Error: in parsing index file \""+
                 std::string(filename)+"\".\n",
                 INPUT_ERROR);
    }

    int atom_number = 1;
    size_t pos = is.tellg();
    while ( (is >> atom_number) && (atom_number > 0) ) {
      (index_groups.back()).push_back(atom_number);
      pos = is.tellg();
    }
    is.clear();
    is.seekg(pos, std::ios::beg);
    std::string delim;
    if ( (is >> delim) && (delim == "[") ) {
      // new group
      is.clear();
      is.seekg(pos, std::ios::beg);
    } else {
      break;
    }
  }

  cvm::log("The following index groups were read from the index file \""+
           std::string(filename)+"\":\n");
  std::list<std::string>::iterator names_i = index_group_names.begin();
  std::list<std::vector<int> >::iterator lists_i = index_groups.begin();
  for ( ; names_i != index_group_names.end() ; names_i++, lists_i++) {
    cvm::log("  "+(*names_i)+" ("+cvm::to_str(lists_i->size())+" atoms).\n");
  }
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}


int cvm::load_atoms(char const *file_name,
                    cvm::atom_group &atoms,
                    std::string const &pdb_field,
                    double pdb_field_value)
{
  return proxy->load_atoms(file_name, atoms, pdb_field, pdb_field_value);
}


int cvm::load_coords(char const *file_name,
                     std::vector<cvm::rvector> *pos,
                     cvm::atom_group *atoms,
                     std::string const &pdb_field,
                     double pdb_field_value)
{
  int error_code = COLVARS_OK;

  std::string const ext(strlen(file_name) > 4 ?
                        (file_name + (strlen(file_name) - 4)) :
                        file_name);

  atoms->create_sorted_ids();

  std::vector<cvm::rvector> sorted_pos(atoms->size(), cvm::rvector(0.0));

  // Differentiate between PDB and XYZ files
  if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) {
    if (pdb_field.size() > 0) {
      return cvm::error("Error: PDB column may not be specified "
                        "for XYZ coordinate files.\n", INPUT_ERROR);
    }
    // For XYZ files, use internal parser
    error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms);
  } else {
    // Otherwise, call proxy function for PDB
    error_code |= proxy->load_coords(file_name,
                                     sorted_pos, atoms->sorted_ids(),
                                     pdb_field, pdb_field_value);
  }

  std::vector<int> const &map = atoms->sorted_ids_map();
  for (size_t i = 0; i < atoms->size(); i++) {
    (*pos)[map[i]] = sorted_pos[i];
  }

  return error_code;
}


int cvm::load_coords_xyz(char const *filename,
                         std::vector<rvector> *pos,
                         cvm::atom_group *atoms)
{
  std::ifstream xyz_is(filename);
  unsigned int natoms;
  char symbol[256];
  std::string line;

  if ( ! (xyz_is >> natoms) ) {
    cvm::error("Error: cannot parse XYZ file "
               + std::string(filename) + ".\n", INPUT_ERROR);
  }
  // skip comment line
  cvm::getline(xyz_is, line);
  cvm::getline(xyz_is, line);
  xyz_is.width(255);
  std::vector<atom_pos>::iterator pos_i = pos->begin();

  if (pos->size() != natoms) { // Use specified indices
    int next = 0; // indices are zero-based
    std::vector<int>::const_iterator index = atoms->sorted_ids().begin();
    for ( ; pos_i != pos->end() ; pos_i++, index++) {

      while ( next < *index ) {
        cvm::getline(xyz_is, line);
        next++;
      }
      xyz_is >> symbol;
      xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
    }
  } else {          // Use all positions
    for ( ; pos_i != pos->end() ; pos_i++) {
      xyz_is >> symbol;
      xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
    }
  }
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}



// Wrappers to proxy functions: these may go in the future

cvm::real cvm::unit_angstrom()
{
  return proxy->unit_angstrom();
}


cvm::real cvm::boltzmann()
{
  return proxy->boltzmann();
}


cvm::real cvm::temperature()
{
  return proxy->temperature();
}


cvm::real cvm::dt()
{
  return proxy->dt();
}


void cvm::request_total_force()
{
  proxy->request_total_force(true);
}


cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1,
                                    cvm::atom_pos const &pos2)
{
  return proxy->position_distance(pos1, pos2);
}


cvm::real cvm::rand_gaussian(void)
{
  return proxy->rand_gaussian();
}



bool cvm::replica_enabled()
{
  return proxy->replica_enabled();
}

int cvm::replica_index()
{
  return proxy->replica_index();
}

int cvm::replica_num()
{
  return proxy->replica_num();
}

void cvm::replica_comm_barrier()
{
  return proxy->replica_comm_barrier();
}

int cvm::replica_comm_recv(char* msg_data, int buf_len, int src_rep)
{
  return proxy->replica_comm_recv(msg_data,buf_len,src_rep);
}

int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep)
{
  return proxy->replica_comm_send(msg_data,msg_len,dest_rep);
}



template<typename T> std::string _to_str(T const &x,
                                         size_t width, size_t prec)
{
  std::ostringstream os;
  if (width) os.width(width);
  if (prec) {
    os.setf(std::ios::scientific, std::ios::floatfield);
    os.precision(prec);
  }
  os << x;
  return os.str();
}


template<typename T> std::string _to_str_vector(std::vector<T> const &x,
                                                size_t width, size_t prec)
{
  if (!x.size()) return std::string("");
  std::ostringstream os;
  if (prec) {
    os.setf(std::ios::scientific, std::ios::floatfield);
  }
  os << "{ ";
  if (width) os.width(width);
  if (prec) os.precision(prec);
  os << x[0];
  for (size_t i = 1; i < x.size(); i++) {
    os << ", ";
    if (width) os.width(width);
    if (prec) os.precision(prec);
    os << x[i];
  }
  os << " }";
  return os.str();
}



std::string colvarmodule::to_str(std::string const &x)
{
  return std::string("\"")+x+std::string("\"");
}

std::string colvarmodule::to_str(char const *x)
{
  return std::string("\"")+std::string(x)+std::string("\"");
}

std::string colvarmodule::to_str(bool x)
{
  return (x ? "on" : "off");
}

std::string colvarmodule::to_str(int const &x,
                                 size_t width, size_t prec)
{
  return _to_str<int>(x, width, prec);
}

std::string colvarmodule::to_str(size_t const &x,
                                 size_t width, size_t prec)
{
  return _to_str<size_t>(x, width, prec);
}

std::string colvarmodule::to_str(long int const &x,
                                 size_t width, size_t prec)
{
  return _to_str<long int>(x, width, prec);
}

std::string colvarmodule::to_str(step_number const &x,
                                 size_t width, size_t prec)
{
  return _to_str<step_number>(x, width, prec);
}

std::string colvarmodule::to_str(cvm::real const &x,
                                 size_t width, size_t prec)
{
  return _to_str<cvm::real>(x, width, prec);
}

std::string colvarmodule::to_str(cvm::rvector const &x,
                                 size_t width, size_t prec)
{
  return _to_str<cvm::rvector>(x, width, prec);
}

std::string colvarmodule::to_str(cvm::quaternion const &x,
                                 size_t width, size_t prec)
{
  return _to_str<cvm::quaternion>(x, width, prec);
}

std::string colvarmodule::to_str(colvarvalue const &x,
                                 size_t width, size_t prec)
{
  return _to_str<colvarvalue>(x, width, prec);
}

std::string colvarmodule::to_str(cvm::vector1d<cvm::real> const &x,
                                 size_t width, size_t prec)
{
  return _to_str< cvm::vector1d<cvm::real> >(x, width, prec);
}

std::string colvarmodule::to_str(cvm::matrix2d<cvm::real> const &x,
                                 size_t width, size_t prec)
{
  return _to_str< cvm::matrix2d<cvm::real> >(x, width, prec);
}


std::string colvarmodule::to_str(std::vector<int> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<int>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<size_t> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<size_t>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<long int> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<long int>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<cvm::real> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<cvm::real>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<cvm::rvector> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<cvm::rvector>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<cvm::quaternion> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<cvm::quaternion>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<colvarvalue> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<colvarvalue>(x, width, prec);
}

std::string colvarmodule::to_str(std::vector<std::string> const &x,
                                 size_t width, size_t prec)
{
  return _to_str_vector<std::string>(x, width, prec);
}


std::string cvm::wrap_string(std::string const &s, size_t nchars)
{
  if (!s.size()) {
    return std::string(nchars, ' ');
  } else {
    return ( (s.size() <= nchars) ?
             (s+std::string(nchars-s.size(), ' ')) :
             (std::string(s, 0, nchars)) );
  }
}


// shared pointer to the proxy object
colvarproxy *colvarmodule::proxy = NULL;

// static runtime data
cvm::real colvarmodule::debug_gradients_step_size = 1.0e-07;
int       colvarmodule::errorCode = 0;
int       colvarmodule::log_level_ = 10;
cvm::step_number colvarmodule::it = 0;
cvm::step_number colvarmodule::it_restart = 0;
size_t    colvarmodule::restart_out_freq = 0;
size_t    colvarmodule::cv_traj_freq = 0;
bool      colvarmodule::use_scripted_forces = false;
bool      colvarmodule::scripting_after_biases = true;

// i/o constants
size_t const colvarmodule::it_width = 12;
size_t const colvarmodule::cv_prec  = 14;
size_t const colvarmodule::cv_width = 21;
size_t const colvarmodule::en_prec  = 14;
size_t const colvarmodule::en_width = 21;
const char * const colvarmodule::line_marker = (const char *)
  "----------------------------------------------------------------------\n";