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colvarmodule.cpp
12f3178e868dlammm-master-deprecated

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_abf.h"
			#include "colvarbias_alb.h"
			#include "colvarbias_histogram.h"
			#include "colvarbias_meta.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");
			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;
			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)
			{
			// 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();
			}

			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 get_error();
			}


			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);

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

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

			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(keyword));
			biases.back()->init(bias_conf);
			if (cvm::check_new_bias(bias_conf, keyword) != COLVARS_OK) {
			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();
			}

			size_t i;

			for (i = 0; i < biases.size(); i++) {
			biases[i]->enable(cvm::deps::f_cvb_active);
			if (cvm::debug())
			biases[i]->print_state();
			}

			size_t n_hist_dep_biases = 0;
			for (i = 0; i < biases.size(); i++) {
			if (biases[i]->is_enabled(cvm::deps::f_cvb_apply_force) &&
			biases[i]->is_enabled(cvm::deps::f_cvb_history_dependent)) {
			n_hist_dep_biases++;
			}
			}
			if (n_hist_dep_biases) {
			cvm::log("WARNING: there are "+cvm::to_str(n_hist_dep_biases)+
			" history-dependent biases with non-zero force parameters; "
			"please make sure that their forces do not counteract each other.\n");
			}

			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);
			}


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

			combine_errors(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();
			}
			combine_errors(error_code, calc_biases());
			combine_errors(error_code, update_colvar_forces());

			if (cvm::b_analysis) {
			combine_errors(error_code, analyze());
			}

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

			// write restart files, if needed
			if (restart_out_freq && restart_out_name.size()) {
			combine_errors(error_code, write_restart_files());
			}

			return error_code;
			}


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

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

			// Determine which colvars are active at this time step
			for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
			(cvi)->feature_states[cvm::deps::f_cv_active]->enabled = (step_absolute() % (cvi)->get_time_step_factor() == 0);
			}

			// 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

			colvars_smp.resize(0);
			colvars_smp_items.resize(0);

			colvars_smp.reserve(colvars.size());
			colvars_smp_items.reserve(colvars.size());

			// set up a vector containing all components
			size_t num_colvar_items = 0;
			cvm::increase_depth();
			for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {

			if (!(*cvi)->is_enabled()) continue;
			combine_errors(error_code, (*cvi)->update_cvc_flags());

			size_t num_items = (*cvi)->num_active_cvcs();
			colvars_smp.reserve(colvars_smp.size() + num_items);
			colvars_smp_items.reserve(colvars_smp_items.size() + num_items);
			for (size_t icvc = 0; icvc < num_items; icvc++) {
			colvars_smp.push_back(*cvi);
			colvars_smp_items.push_back(icvc);
			}

			num_colvar_items += num_items;
			}
			cvm::decrease_depth();

			// calculate colvar components in parallel
			combine_errors(error_code, proxy->smp_colvars_loop());

			cvm::increase_depth();
			for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
			if (!(*cvi)->is_enabled()) continue;
			combine_errors(error_code, (*cvi)->collect_cvc_data());
			}
			cvm::decrease_depth();

			} else {

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

			combine_errors(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() && biases.size())
			cvm::log("Updating collective variable biases.\n");

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

			// 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
			combine_errors(error_code, proxy->smp_biases_script_loop());
			} else {
			// calculate biases in parallel
			combine_errors(error_code, proxy->smp_biases_loop());
			}

			} else {

			if (use_scripted_forces && !scripting_after_biases) {
			combine_errors(error_code, calc_scripted_forces());
			}

			cvm::increase_depth();
			for (bi = biases.begin(); bi != biases.end(); bi++) {
			combine_errors(error_code, (*bi)->update());
			if (cvm::get_error()) {
			return COLVARS_ERROR;
			}
			}
			cvm::decrease_depth();
			}

			cvm::real total_bias_energy = 0.0;
			for (bi = biases.begin(); bi != biases.end(); bi++) {
			total_bias_energy += (*bi)->get_energy();
			}

			proxy->add_energy(total_bias_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() && biases.size())
			cvm::log("Collecting forces from all biases.\n");
			cvm::increase_depth();
			for (bi = biases.begin(); bi != biases.end(); bi++) {
			(*bi)->communicate_forces();
			if (cvm::get_error()) {
			return COLVARS_ERROR;
			}
			}
			cvm::decrease_depth();

			if (use_scripted_forces && scripting_after_biases) {
			combine_errors(error_code, calc_scripted_forces());
			}

			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 = colvars.begin(); cvi != colvars.end(); cvi++) {
			// Here we call even inactive colvars, so they accumulate biasing forces
			// as well as update their extended-system dynamics
			total_colvar_energy += (*cvi)->update_forces_energy();
			if (cvm::get_error()) {
			return COLVARS_ERROR;
			}
			}
			cvm::decrease_depth();
			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 = colvars.begin(); cvi != colvars.end(); cvi++) {
			if ((*cvi)->is_enabled(cvm::deps::f_cv_gradient)) {
			if (!(*cvi)->is_enabled()) continue;
			(*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_files()
			{
			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();
			}

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


			int colvarmodule::write_traj_files()
			{
			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();
			}
			}

			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)->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::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()
			{
			if ((proxy->smp_thread_id() == COLVARS_NOT_IMPLEMENTED) \|\|
			(proxy->smp_thread_id() == 0)) {
			reset();
			delete parse;
			parse = NULL;
			proxy = NULL;
			}
			}


			int colvarmodule::reset()
			{
			parse->init();

			cvm::log("Resetting the Collective Variables Module.\n");

			// 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();

			// 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();

			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()
			{
			int error_code = 0;

			// 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()) {
			combine_errors(error_code, open_traj_file(cv_traj_name));
			}

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

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

			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;
			}
			std::string restart_version;
			parse->get_keyval(restart_conf, "version",
			restart_version, std::string(""),
			colvarparse::parse_silent);
			if (restart_version.size() && (restart_version != std::string(COLVARS_VERSION))) {
			cvm::log("This state file was generated with version "+restart_version+"\n");
			}
			}
			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_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();

			cvm::increase_depth();
			for (std::vector<colvarbias *>::iterator bi = biases.begin();
			bi != biases.end();
			bi++) {
			(*bi)->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,
			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";

			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.is_open()) {
			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)
			{
			size_t const d = depth();
			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
			size_t const nt = proxy->smp_num_threads();
			if (proxy->smp_enabled() == COLVARS_OK) {
			if (depth_v.size() != nt) {
			// update array of depths
			proxy->smp_lock();
			if (depth_v.size() > 0) { depth_s = depth_v[0]; }
			depth_v.clear();
			depth_v.assign(nt, depth_s);
			proxy->smp_unlock();
			}
			return depth_v[proxy->smp_thread_id()];
			}
			return depth_s;
			}


			void colvarmodule::set_error_bit(int code)
			{
			if (code > 0) {
			cvm::fatal_error("Error: set_error_bit() received positive error code.\n");
			return;
			}
			proxy->smp_lock();
			errorCode = -1 * ((-1 * errorCode) \| (-1 * code) \| (-1 * COLVARS_ERROR));
			proxy->smp_unlock();
			}

			bool colvarmodule::get_error_bit(int code)
			{
			return bool((-1 * errorCode) & (-1 * code));
			}

			void colvarmodule::combine_errors(int &target, int const code)
			{
			if (code > 0 \|\| target > 0) {
			cvm::fatal_error("Error: combine_errors() received positive error code.\n");
			return;
			}
			target = -1 * ((-1 * target) \| (-1 * code));
			}

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


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


			void cvm::fatal_error(std::string const &message)
			{
			// TODO once all non-fatal errors have been set to be handled by error(),
			// set DELETE_COLVARS here for VMD to handle it
			set_error_bit(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,
			cvm::atom_group &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-07;
			int colvarmodule::errorCode = 0;
			long colvarmodule::it = 0;
			long colvarmodule::it_restart = 0;
			size_t colvarmodule::restart_out_freq = 0;
			size_t colvarmodule::cv_traj_freq = 0;
			size_t colvarmodule::depth_s = 0;
			std::vector<size_t> colvarmodule::depth_v(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;
			bool colvarmodule::scripting_after_biases = true;

			// 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";

lammps/lib/colvars/colvarmodule.cpp12f3178e868dlammm-master-deprecated

colvarmodule.cppView Options

lammps/lib/colvars/colvarmodule.cpp
12f3178e868dlammm-master-deprecated

colvarmodule.cpp
View Options