colvarmodule.cpp
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Created: Wed, May 22, 13:46

colvarmodule.cpp
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	/// -- c++ --

	#include <sstream>
	#include <string.h>

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

	colvarmodule::colvarmodule(colvarproxy *proxy_in)
	{
	// pointer to the proxy object
	if (proxy == NULL) {
	proxy = proxy_in;
	parse = new colvarparse();
	} 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");
	return;
	}
	cvm::log(cvm::line_marker);
	cvm::log("Initializing the collective variables module, version "+
	cvm::to_str(COLVARS_VERSION)+".\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;
	colvarmodule::it_restart_from_state_file = true;

	colvarmodule::use_scripted_forces = false;

	colvarmodule::b_analysis = false;

	colvarmodule::debug_gradients_step_size = 1.0e-07;

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

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

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


	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 (colvarparse::getline_nocomments(config_s, line)) {
	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 config_s(config_str);

	// strip the comments away
	std::string conf = "";
	std::string line;
	while (colvarparse::getline_nocomments(config_s, line)) {
	conf.append(line+"\n");
	}
	return parse_config(conf);
	}

	int colvarmodule::parse_config(std::string &conf)
	{
	int error_code = 0;

	// parse global options
	error_code \|= parse_global_params(conf);

	if (error_code != COLVARS_OK \|\| cvm::get_error()) {
	set_error_bits(INPUT_ERROR);
	return COLVARS_ERROR;
	}

	// parse the options for collective variables
	error_code \|= parse_colvars(conf);

	if (error_code != COLVARS_OK \|\| cvm::get_error()) {
	set_error_bits(INPUT_ERROR);
	return COLVARS_ERROR;
	}

	// parse the options for biases
	error_code \|= parse_biases(conf);

	if (error_code != COLVARS_OK \|\| cvm::get_error()) {
	set_error_bits(INPUT_ERROR);
	return COLVARS_ERROR;
	}

	// done parsing known keywords, check that all keywords found were valid ones
	error_code \|= parse->check_keywords(conf, "colvarmodule");

	if (error_code != COLVARS_OK \|\| cvm::get_error()) {
	set_error_bits(INPUT_ERROR);
	return COLVARS_ERROR;
	}

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

	if (cv_traj_os.is_open()) {
	// configuration might have changed, better redo the labels
	write_traj_label(cv_traj_os);
	}

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


	int colvarmodule::parse_global_params(std::string const &conf)
	{
	std::string index_file_name;
	if (parse->get_keyval(conf, "indexFile", index_file_name)) {
	read_index_file(index_file_name.c_str());
	}

	parse->get_keyval(conf, "analysis", b_analysis, b_analysis);

	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);

	// if this is true when initializing, it means
	// we are continuing after a reset(): default to true
	parse->get_keyval(conf, "colvarsTrajAppend", cv_traj_append, cv_traj_append);

	parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false,
	colvarparse::parse_silent);

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

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


	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(colvar_conf));
	if (cvm::get_error() \|\|
	((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,
	size_t &bias_count)
	{
	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(bias_conf, keyword));
	if (cvm::check_new_bias(bias_conf, keyword)) {
	return COLVARS_ERROR;
	}
	cvm::decrease_depth();
	bias_count++;
	} 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", n_abf_biases);

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

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

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

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

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

	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();
	}

	if (biases.size() \|\| use_scripted_forces) {
	cvm::log(cvm::line_marker);
	cvm::log("Collective variables biases initialized, "+
	cvm::to_str(biases.size())+" 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);
	}


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


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


	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); }
	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::fatal_error("Error: colvar not found: " + name); }
	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::fatal_error("Error: bias not found: " + bias_name); }
	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() {
	cvm::real total_bias_energy = 0.0;
	cvm::real total_colvar_energy = 0.0;

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

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

	// calculate collective variables and their gradients
	if (cvm::debug())
	cvm::log("Calculating collective variables.\n");
	cvm::increase_depth();
	for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
	(*cvi)->calc();
	if (cvm::get_error()) {
	return COLVARS_ERROR;
	}
	}
	cvm::decrease_depth();

	// update the biases and communicate their forces to the collective
	// variables
	if (cvm::debug() && biases.size())
	cvm::log("Updating collective variable biases.\n");
	cvm::increase_depth();
	for (bi = biases.begin(); bi != biases.end(); bi++) {
	total_bias_energy += (*bi)->update();
	if (cvm::get_error()) {
	return COLVARS_ERROR;
	}
	}
	cvm::decrease_depth();

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

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

	cvm::decrease_depth();

	if (cvm::b_analysis) {
	// perform runtime analysis of colvars and biases
	if (cvm::debug() && biases.size())
	cvm::log("Perform runtime analyses.\n");
	cvm::increase_depth();
	for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
	(*cvi)->analyse();
	if (cvm::get_error()) {
	return COLVARS_ERROR;
	}
	}
	for (bi = biases.begin(); bi != biases.end(); bi++) {
	(*bi)->analyse();
	if (cvm::get_error()) {
	return COLVARS_ERROR;
	}
	}
	cvm::decrease_depth();
	}

	// 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 = colvars.begin(); cvi != colvars.end(); cvi++) {
	total_colvar_energy += (*cvi)->update();
	if (cvm::get_error()) {
	return COLVARS_ERROR;
	}
	}
	cvm::decrease_depth();
	proxy->add_energy(total_bias_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 = colvars.begin(); cvi != colvars.end(); cvi++) {
	if ((*cvi)->tasks[colvar::task_gradients]) {
	(*cvi)->communicate_forces();
	if (cvm::get_error()) {
	return COLVARS_ERROR;
	}
	}
	}
	cvm::decrease_depth();

	// write restart file, if needed
	if (restart_out_freq && restart_out_name.size()) {
	if ( (cvm::step_relative() > 0) &&
	((cvm::step_absolute() % restart_out_freq) == 0) ) {
	cvm::log("Writing the state file \""+
	restart_out_name+"\".\n");
	proxy->backup_file(restart_out_name.c_str());
	restart_out_os.open(restart_out_name.c_str());
	if (!restart_out_os.is_open() \|\| !write_restart(restart_out_os))
	cvm::error("Error: in writing restart file.\n");
	restart_out_os.close();
	}
	}

	// write trajectory file, if needed
	if (cv_traj_freq && cv_traj_name.size()) {

	if (!cv_traj_os.is_open()) {
	open_traj_file(cv_traj_name);
	}

	// 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) {
	write_traj_label(cv_traj_os);
	}

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

	if (restart_out_freq && cv_traj_os.is_open()) {
	// 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");
	cv_traj_os.flush();
	}
	}
	} // end if (cv_traj_freq)

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


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

	if (cvm::step_relative() == 0)
	cvm::log("Performing analysis.\n");

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

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

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

	int colvarmodule::setup()
	{
	// loop over all components of all colvars to reset masses of all groups
	for (std::vector<colvar *>::iterator cvi = colvars.begin();
	cvi != colvars.end(); cvi++) {
	(*cvi)->setup();
	}
	return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);

	}

	colvarmodule::~colvarmodule()
	{
	reset();
	delete parse;
	proxy = NULL;
	}

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

	// 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();

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

	if (cv_traj_os.is_open()) {
	// Do not close file here, as we might not be done with it yet.
	cv_traj_os.flush();
	}

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


	int colvarmodule::setup_input()
	{
	// name of input state file
	restart_in_name = proxy->input_prefix().size() ?
	std::string(proxy->input_prefix()+".colvars.state") :
	std::string("") ;

	// read the restart configuration, if available
	if (restart_in_name.size()) {
	// read the restart file
	std::ifstream input_is(restart_in_name.c_str());
	if (!input_is.good()) {
	cvm::error("Error: in opening restart file \""+
	std::string(restart_in_name)+"\".\n",
	FILE_ERROR);
	return COLVARS_ERROR;
	} else {
	cvm::log("Restarting from file \""+restart_in_name+"\".\n");
	read_restart(input_is);
	if (cvm::get_error() != COLVARS_OK) {
	return COLVARS_ERROR;
	}
	cvm::log(cvm::line_marker);
	}
	}
	return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);

	}


	int colvarmodule::setup_output()
	{
	// 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()) {
	open_traj_file(cv_traj_name);
	}

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


	std::istream & colvarmodule::read_restart(std::istream &is)
	{
	{
	// read global restart information
	std::string restart_conf;
	if (is >> colvarparse::read_block("configuration", restart_conf)) {
	if (it_restart_from_state_file) {
	parse->get_keyval(restart_conf, "step",
	it_restart, (size_t) 0,
	colvarparse::parse_silent);
	it = it_restart;
	}
	}
	is.clear();
	}

	// 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_restart(is))) {
	cvm::error("Error: in reading restart configuration for bias \""+
	(*bi)->name+"\".\n",
	INPUT_ERROR);
	}
	}
	cvm::decrease_depth();

	return is;
	}


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


	int colvarmodule::write_output_files()
	{
	// if this is a simulation run (i.e. not a postprocessing), output data
	// must be written to be able to restart the simulation
	std::string const out_name =
	(output_prefix.size() ?
	std::string(output_prefix+".colvars.state") :
	std::string("colvars.state"));
	cvm::log("Saving collective variables state to \""+out_name+"\".\n");

	std::ostream * os = proxy->output_stream(out_name);
	os->setf(std::ios::scientific, std::ios::floatfield);
	this->write_restart(*os);
	proxy->close_output_stream(out_name);

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

	if (cv_traj_os.is_open()) {
	// do not close to avoid problems with multiple NAMD runs
	cv_traj_os.flush();
	}

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



	int colvarmodule::read_traj(char const *traj_filename,
	size_t traj_read_begin,
	size_t 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"
	<< "}\n\n";

	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_restart(os);
	}
	cvm::decrease_depth();

	return os;
	}

	int colvarmodule::open_traj_file(std::string const &file_name)
	{
	if (cv_traj_os.is_open()) {
	return COLVARS_OK;
	}

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

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

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

	int colvarmodule::close_traj_file()
	{
	if (cv_traj_os.good()) {
	cv_traj_os.close();
	}
	return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
	}

	std::ostream & colvarmodule::write_traj_label(std::ostream &os)
	{
	if (!os.good()) {
	cvm::error("Cannot write to trajectory file.");
	return 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()) {
	os.flush();
	}
	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()) {
	os.flush();
	}
	cvm::decrease_depth();
	return os;
	}


	void cvm::log(std::string const &message)
	{
	if (depth > 0)
	proxy->log((std::string(2*depth, ' '))+message);
	else
	proxy->log(message);
	}

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

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

	void cvm::error(std::string const &message, int code)
	{
	set_error_bits(code);
	proxy->error(message);
	}

	void cvm::fatal_error(std::string const &message)
	{
	set_error_bits(FATAL_ERROR);
	proxy->fatal_error(message);
	}

	void cvm::exit(std::string const &message)
	{
	proxy->exit(message);
	}


	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);
	}
	}
	cvm::index_group_names.push_back(group_name);
	cvm::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) ) {
	(cvm::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,
	std::vector<cvm::atom> &atoms,
	std::string const &pdb_field,
	double const 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::atom_pos> &pos,
	const std::vector<int> &indices,
	std::string const &pdb_field,
	double const pdb_field_value)
	{
	// Differentiate between PDB and XYZ files
	// for XYZ files, use CVM internal parser
	// otherwise call proxy function for PDB

	std::string const ext(strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name);
	if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) {
	if ( pdb_field.size() > 0 ) {
	cvm::error("Error: PDB column may not be specified for XYZ coordinate file.\n", INPUT_ERROR);
	return COLVARS_ERROR;
	}
	return cvm::load_coords_xyz(file_name, pos, indices);
	} else {
	return proxy->load_coords(file_name, pos, indices, pdb_field, pdb_field_value);
	}
	}


	int cvm::load_coords_xyz(char const *filename,
	std::vector<atom_pos> &pos,
	const std::vector<int> &indices)
	{
	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
	std::getline(xyz_is, line);
	std::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 = indices.begin();
	for ( ; pos_i != pos.end() ; pos_i++, index++) {

	while ( next < *index ) {
	std::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);
	}

	// static pointers
	std::vector<colvar *> colvarmodule::colvars;
	std::vector<colvarbias *> colvarmodule::biases;
	size_t colvarmodule::n_abf_biases = 0;
	size_t colvarmodule::n_rest_biases = 0;
	size_t colvarmodule::n_histo_biases = 0;
	size_t colvarmodule::n_meta_biases = 0;
	colvarproxy *colvarmodule::proxy = NULL;


	// static runtime data
	cvm::real colvarmodule::debug_gradients_step_size = 1.0e-03;
	int colvarmodule::errorCode = 0;
	size_t colvarmodule::it = 0;
	size_t colvarmodule::it_restart = 0;
	size_t colvarmodule::restart_out_freq = 0;
	size_t colvarmodule::cv_traj_freq = 0;
	size_t colvarmodule::depth = 0;
	bool colvarmodule::b_analysis = false;
	std::list<std::string> colvarmodule::index_group_names;
	std::list<std::vector<int> > colvarmodule::index_groups;
	bool colvarmodule::use_scripted_forces = false;

	// file name prefixes
	std::string colvarmodule::output_prefix = "";
	std::string colvarmodule::restart_in_name = "";


	// 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;
	std::string const colvarmodule::line_marker =
	"----------------------------------------------------------------------\n";

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