colvardeps.cpp
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Created: Tue, Jun 4, 21:28

colvardeps.cpp
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	// -- 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 "colvardeps.h"

	colvardeps::colvardeps()
	: time_step_factor (1) {}

	colvardeps::~colvardeps() {
	size_t i;

	// Protest if we are deleting an object while a parent object may still depend on it
	if (parents.size()) {
	cvm::log("Warning: destroying \"" + description + "\" before its parents objects:");
	for (i=0; i<parents.size(); i++) {
	cvm::log(parents[i]->description);
	}
	}

	// Do not delete features if it's a static object
	// may change in the future though
	// for (i=0; i<features.size(); i++) {
	// if (features[i] != NULL) delete features[i];
	// }

	remove_all_children();
	}


	void colvardeps::free_children_deps() {
	// Dereference children requirements of all enabled features
	// Useful when object is destroyed or set inactive
	// CAUTION: when setting the parent object inactive, disable "active" first
	// then call this, to avoid double-dereferencing the deps of "active"

	// Cannot be in the base class destructor because it needs the derived class features()
	size_t i,j,fid;

	if (cvm::debug()) cvm::log("DEPS: freeing children deps for " + description);

	cvm::increase_depth();
	for (fid = 0; fid < feature_states.size(); fid++) {
	if (is_enabled(fid)) {
	for (i=0; i<features()[fid]->requires_children.size(); i++) {
	int g = features()[fid]->requires_children[i];
	for (j=0; j<children.size(); j++) {
	if (cvm::debug()) cvm::log("DEPS: dereferencing children's "
	+ children[j]->features()[g]->description);
	children[j]->decr_ref_count(g);
	}
	}
	}
	}
	cvm::decrease_depth();
	}


	// re-enable children features (and increase ref count accordingly)
	// So free_children_deps() can be called whenever an object becomes inactive
	void colvardeps::restore_children_deps() {
	size_t i,j,fid;

	cvm::increase_depth();
	for (fid = 0; fid < feature_states.size(); fid++) {
	if (is_enabled(fid)) {
	for (i=0; i<features()[fid]->requires_children.size(); i++) {
	int g = features()[fid]->requires_children[i];
	for (j=0; j<children.size(); j++) {
	if (cvm::debug()) cvm::log("DEPS: re-enabling children's "
	+ children[j]->features()[g]->description);
	children[j]->enable(g, false, false);
	}
	}
	}
	}
	cvm::decrease_depth();
	}


	void colvardeps::provide(int feature_id, bool truefalse) {
	feature_states[feature_id].available = truefalse;
	}


	void colvardeps::set_enabled(int feature_id, bool truefalse) {
	if (truefalse) {
	enable(feature_id);
	} else {
	disable(feature_id);
	}
	}


	bool colvardeps::get_keyval_feature(colvarparse *cvp,
	std::string const &conf, char const *key,
	int feature_id, bool const &def_value,
	colvarparse::Parse_Mode const parse_mode)
	{
	if (!is_user(feature_id)) {
	cvm::error("Cannot set feature \"" + features()[feature_id]->description + "\" from user input in \"" + description + "\".\n");
	return false;
	}
	bool value;
	bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode);
	if (value) enable(feature_id);
	return found;
	}


	int colvardeps::enable(int feature_id,
	bool dry_run /* default: false */,
	// dry_run: fail silently, do not enable if available
	// flag is passed recursively to deps of this feature
	bool toplevel /* default: true */)
	// toplevel: false if this is called as part of a chain of dependency resolution
	// this is used to diagnose failed dependencies by displaying the full stack
	// only the toplevel dependency will throw a fatal error
	{
	int res;
	size_t i, j;
	bool ok;
	feature *f = features()[feature_id];
	feature_state *fs = &feature_states[feature_id];

	if (cvm::debug()) {
	cvm::log("DEPS: " + description +
	(dry_run ? " testing " : " enabling ") +
	"\"" + f->description +"\"");
	}

	if (fs->enabled) {
	if (!(dry_run \|\| toplevel)) {
	// This is a dependency
	// Prevent disabling this feature as long
	// as requirement is enabled
	fs->ref_count++;
	if (cvm::debug())
	cvm::log("DEPS: bumping ref_count to " + cvm::to_str(fs->ref_count));
	}
	// Do not try to further resolve deps
	return COLVARS_OK;
	}

	std::string feature_type_descr = is_static(feature_id) ? "Static" :
	(is_dynamic(feature_id) ? "Dynamic" : "User-controlled");

	if (!fs->available) {
	if (!dry_run) {
	if (toplevel) {
	cvm::error("Error: " + feature_type_descr + " feature unavailable: \""
	+ f->description + "\" in " + description + ".");
	} else {
	cvm::log(feature_type_descr + " feature unavailable: \""
	+ f->description + "\" in " + description + ".");
	}
	}
	return COLVARS_ERROR;
	}

	if (!toplevel && !is_dynamic(feature_id)) {
	if (!dry_run) {
	cvm::log(feature_type_descr + " feature \"" + f->description
	+ "\" may not be enabled as a dependency in " + description + ".\n");
	}
	return COLVARS_ERROR;
	}

	// 1) enforce exclusions
	// reminder: exclusions must be mutual for this to work
	for (i=0; i<f->requires_exclude.size(); i++) {
	feature *g = features()[f->requires_exclude[i]];
	if (cvm::debug())
	cvm::log(f->description + " requires exclude " + g->description);
	if (is_enabled(f->requires_exclude[i])) {
	if (!dry_run) {
	cvm::log("Feature \"" + f->description + "\" is incompatible with \""
	+ g->description + "\" in " + description + ".");
	if (toplevel) {
	cvm::error("Error: Failed dependency in " + description + ".");
	}
	}
	return COLVARS_ERROR;
	}
	}

	// 2) solve internal deps (self)
	for (i=0; i<f->requires_self.size(); i++) {
	if (cvm::debug())
	cvm::log(f->description + " requires self " + features()[f->requires_self[i]]->description);
	res = enable(f->requires_self[i], dry_run, false);
	if (res != COLVARS_OK) {
	if (!dry_run) {
	cvm::log("...required by \"" + f->description + "\" in " + description);
	if (toplevel) {
	cvm::error("Error: Failed dependency in " + description + ".");
	}
	}
	return res;
	}
	}

	// 3) solve internal alternate deps
	for (i=0; i<f->requires_alt.size(); i++) {

	// test if one is available; if yes, enable and exit w/ success
	ok = false;
	for (j=0; j<f->requires_alt[i].size(); j++) {
	int g = f->requires_alt[i][j];
	if (cvm::debug())
	cvm::log(f->description + " requires alt " + features()[g]->description);
	res = enable(g, true, false); // see if available
	if (res == COLVARS_OK) {
	ok = true;
	if (!dry_run) {
	enable(g, false, false); // Require again, for real
	fs->alternate_refs.push_back(g); // We remember we enabled this
	// so we can free it if this feature gets disabled
	}
	break;
	}
	}
	if (!ok) {
	if (!dry_run) {
	cvm::log("\"" + f->description + "\" in " + description
	+ " requires one of the following features, none of which can be enabled:\n");
	cvm::log("-----------------------------------------\n");
	cvm::increase_depth();
	for (j=0; j<f->requires_alt[i].size(); j++) {
	int g = f->requires_alt[i][j];
	cvm::log(cvm::to_str(j+1) + ". " + features()[g]->description);
	enable(g, false, false); // Just for printing error output
	}
	cvm::decrease_depth();
	cvm::log("-----------------------------------------");
	if (toplevel) {
	cvm::error("Error: Failed dependency in " + description + ".");
	}
	}
	return COLVARS_ERROR;
	}
	}

	// 4) solve deps in children
	// if the object is inactive, we solve but do not enable: will be enabled
	// when the object becomes active
	cvm::increase_depth();
	for (i=0; i<f->requires_children.size(); i++) {
	int g = f->requires_children[i];
	for (j=0; j<children.size(); j++) {
	res = children[j]->enable(g, dry_run \|\| !is_enabled(), false);
	if (res != COLVARS_OK) {
	if (!dry_run) {
	cvm::log("...required by \"" + f->description + "\" in " + description);
	if (toplevel) {
	cvm::error("Error: Failed dependency in " + description + ".");
	}
	}
	return res;
	}
	}
	}
	cvm::decrease_depth();

	// Actually enable feature only once everything checks out
	if (!dry_run) {
	fs->enabled = true;
	// This should be the only reference
	if (!toplevel) fs->ref_count = 1;
	if (feature_id == 0) {
	// Waking up this object, enable all deps in children
	restore_children_deps();
	}
	do_feature_side_effects(feature_id);
	if (cvm::debug())
	cvm::log("DEPS: feature \"" + f->description + "\" in "
	+ description + " enabled, ref_count = 1.");
	}
	return COLVARS_OK;
	}


	int colvardeps::disable(int feature_id) {
	size_t i, j;
	feature *f = features()[feature_id];
	feature_state *fs = &feature_states[feature_id];

	if (cvm::debug()) cvm::log("DEPS: disabling feature \""
	+ f->description + "\" in " + description);

	if (fs->enabled == false) {
	return COLVARS_OK;
	}

	if (fs->ref_count > 1) {
	cvm::error("Error: cannot disable feature \"" + f->description
	+ "\" in " + description + " because of " + cvm::to_str(fs->ref_count-1)
	+ " remaining references.\n" );
	return COLVARS_ERROR;
	}

	// internal deps (self)
	for (i=0; i<f->requires_self.size(); i++) {
	if (cvm::debug()) cvm::log("DEPS: dereferencing self "
	+ features()[f->requires_self[i]]->description);
	decr_ref_count(f->requires_self[i]);
	}

	// alternates
	for (i=0; i<fs->alternate_refs.size(); i++) {
	if (cvm::debug()) cvm::log("DEPS: dereferencing alt "
	+ features()[fs->alternate_refs[i]]->description);
	decr_ref_count(fs->alternate_refs[i]);
	}
	// Forget these, now that they are dereferenced
	fs->alternate_refs.clear();

	// deps in children
	// except if the object is inactive, then children dependencies
	// have already been dereferenced by this function
	// (or never referenced if feature was enabled while the object
	// was inactive)
	if (is_enabled()) {
	cvm::increase_depth();
	for (i=0; i<f->requires_children.size(); i++) {
	int g = f->requires_children[i];
	for (j=0; j<children.size(); j++) {
	if (cvm::debug()) cvm::log("DEPS: dereferencing children's "
	+ children[j]->features()[g]->description);
	children[j]->decr_ref_count(g);
	}
	}
	cvm::decrease_depth();
	}

	fs->enabled = false;
	fs->ref_count = 0;
	if (feature_id == 0) {
	// Putting this object to sleep
	free_children_deps();
	}
	return COLVARS_OK;
	}

	int colvardeps::decr_ref_count(int feature_id) {
	int &rc = feature_states[feature_id].ref_count;
	feature *f = features()[feature_id];

	if (cvm::debug())
	cvm::log("DEPS: decreasing reference count of \"" + f->description
	+ "\" in " + description + ".\n");

	if (rc <= 0) {
	cvm::error("Error: cannot decrease reference count of feature \"" + f->description
	+ "\" in " + description + ", which is " + cvm::to_str(rc) + ".\n");
	return COLVARS_ERROR;
	}

	rc--;
	if (rc == 0 && f->is_dynamic()) {
	// we can auto-disable this feature
	if (cvm::debug())
	cvm::log("DEPS will now auto-disable dynamic feature \"" + f->description
	+ "\" in " + description + ".\n");
	disable(feature_id);
	}
	return COLVARS_OK;
	}

	void colvardeps::init_feature(int feature_id, const char *description, feature_type type) {
	modify_features()[feature_id]->description = description;
	modify_features()[feature_id]->type = type;
	}

	// Shorthand macros for describing dependencies
	#define f_req_self(f, g) features()[f]->requires_self.push_back(g)
	// This macro ensures that exclusions are symmetric
	#define f_req_exclude(f, g) features()[f]->requires_exclude.push_back(g); \
	features()[g]->requires_exclude.push_back(f)
	#define f_req_children(f, g) features()[f]->requires_children.push_back(g)
	#define f_req_alt2(f, g, h) features()[f]->requires_alt.push_back(std::vector<int>(2));\
	features()[f]->requires_alt.back()[0] = g; \
	features()[f]->requires_alt.back()[1] = h
	#define f_req_alt3(f, g, h, i) features()[f]->requires_alt.push_back(std::vector<int>(3));\
	features()[f]->requires_alt.back()[0] = g; \
	features()[f]->requires_alt.back()[1] = h; \
	features()[f]->requires_alt.back()[2] = i
	#define f_req_alt4(f, g, h, i, j) features()[f]->requires_alt.push_back(std::vector<int>(4));\
	features()[f]->requires_alt.back()[0] = g; \
	features()[f]->requires_alt.back()[1] = h; \
	features()[f]->requires_alt.back()[2] = i; \
	features()[f]->requires_alt.back()[3] = j

	void colvardeps::init_cvb_requires() {
	int i;
	if (features().size() == 0) {
	for (i = 0; i < f_cvb_ntot; i++) {
	modify_features().push_back(new feature);
	}

	init_feature(f_cvb_active, "active", f_type_dynamic);
	f_req_children(f_cvb_active, f_cv_active);

	init_feature(f_cvb_awake, "awake", f_type_static);
	f_req_self(f_cvb_awake, f_cvb_active);

	init_feature(f_cvb_apply_force, "apply force", f_type_user);
	f_req_children(f_cvb_apply_force, f_cv_gradient);

	init_feature(f_cvb_get_total_force, "obtain total force");
	f_req_children(f_cvb_get_total_force, f_cv_total_force);

	init_feature(f_cvb_history_dependent, "history-dependent", f_type_static);

	init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static);
	f_req_children(f_cvb_scalar_variables, f_cv_scalar);

	init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static);
	}

	// Initialize feature_states for each instance
	feature_states.reserve(f_cvb_ntot);
	for (i = 0; i < f_cvb_ntot; i++) {
	feature_states.push_back(feature_state(true, false));
	// Most features are available, so we set them so
	// and list exceptions below
	}
	}


	void colvardeps::init_cv_requires() {
	size_t i;
	if (features().size() == 0) {
	for (i = 0; i < f_cv_ntot; i++) {
	modify_features().push_back(new feature);
	}

	init_feature(f_cv_active, "active", f_type_dynamic);
	// Do not require f_cvc_active in children, as some components may be disabled
	// Colvars must be either a linear combination, or scalar (and polynomial) or scripted/custom
	f_req_alt4(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted, f_cv_custom_function);

	init_feature(f_cv_awake, "awake", f_type_static);
	f_req_self(f_cv_awake, f_cv_active);

	init_feature(f_cv_gradient, "gradient", f_type_dynamic);
	f_req_children(f_cv_gradient, f_cvc_gradient);

	init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic);
	f_req_self(f_cv_collect_gradient, f_cv_gradient);
	f_req_self(f_cv_collect_gradient, f_cv_scalar);
	// The following exlusion could be lifted by implementing the feature
	f_req_exclude(f_cv_collect_gradient, f_cv_scripted);

	init_feature(f_cv_fdiff_velocity, "velocity from finite differences", f_type_dynamic);

	// System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
	init_feature(f_cv_total_force, "total force", f_type_dynamic);
	f_req_alt2(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);

	// Deps for explicit total force calculation
	init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic);
	f_req_self(f_cv_total_force_calc, f_cv_scalar);
	f_req_self(f_cv_total_force_calc, f_cv_linear);
	f_req_children(f_cv_total_force_calc, f_cvc_inv_gradient);
	f_req_self(f_cv_total_force_calc, f_cv_Jacobian);

	init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic);
	f_req_self(f_cv_Jacobian, f_cv_scalar);
	f_req_self(f_cv_Jacobian, f_cv_linear);
	f_req_children(f_cv_Jacobian, f_cvc_Jacobian);

	init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user);
	f_req_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated

	init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user);
	f_req_self(f_cv_extended_Lagrangian, f_cv_scalar);
	f_req_self(f_cv_extended_Lagrangian, f_cv_gradient);

	init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user);
	f_req_self(f_cv_Langevin, f_cv_extended_Lagrangian);

	init_feature(f_cv_linear, "linear", f_type_static);

	init_feature(f_cv_scalar, "scalar", f_type_static);

	init_feature(f_cv_output_energy, "output energy", f_type_user);

	init_feature(f_cv_output_value, "output value", f_type_user);

	init_feature(f_cv_output_velocity, "output velocity", f_type_user);
	f_req_self(f_cv_output_velocity, f_cv_fdiff_velocity);

	init_feature(f_cv_output_applied_force, "output applied force", f_type_user);

	init_feature(f_cv_output_total_force, "output total force", f_type_user);
	f_req_self(f_cv_output_total_force, f_cv_total_force);

	init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user);
	f_req_self(f_cv_subtract_applied_force, f_cv_total_force);
	// There is no well-defined way to implement f_cv_subtract_applied_force
	// in the case of extended-Lagrangian colvars
	f_req_exclude(f_cv_subtract_applied_force, f_cv_extended_Lagrangian);

	init_feature(f_cv_lower_boundary, "lower boundary", f_type_user);
	f_req_self(f_cv_lower_boundary, f_cv_scalar);

	init_feature(f_cv_upper_boundary, "upper boundary", f_type_user);
	f_req_self(f_cv_upper_boundary, f_cv_scalar);

	init_feature(f_cv_grid, "grid", f_type_user);
	f_req_self(f_cv_grid, f_cv_lower_boundary);
	f_req_self(f_cv_grid, f_cv_upper_boundary);

	init_feature(f_cv_runave, "running average", f_type_user);

	init_feature(f_cv_corrfunc, "correlation function", f_type_user);

	init_feature(f_cv_scripted, "scripted", f_type_user);

	init_feature(f_cv_custom_function, "custom function", f_type_user);
	f_req_exclude(f_cv_custom_function, f_cv_scripted);

	init_feature(f_cv_periodic, "periodic", f_type_static);
	f_req_self(f_cv_periodic, f_cv_homogeneous);
	init_feature(f_cv_scalar, "scalar", f_type_static);
	init_feature(f_cv_linear, "linear", f_type_static);
	init_feature(f_cv_homogeneous, "homogeneous", f_type_static);

	// because total forces are obtained from the previous time step,
	// we cannot (currently) have colvar values and total forces for the same timestep
	init_feature(f_cv_multiple_ts, "multiple timestep colvar");
	f_req_exclude(f_cv_multiple_ts, f_cv_total_force_calc);
	}

	// Initialize feature_states for each instance
	feature_states.reserve(f_cv_ntot);
	for (i = 0; i < f_cv_ntot; i++) {
	feature_states.push_back(feature_state(true, false));
	// Most features are available, so we set them so
	// and list exceptions below
	}
	}


	void colvardeps::init_cvc_requires() {
	size_t i;
	// Initialize static array once and for all
	if (features().size() == 0) {
	for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
	modify_features().push_back(new feature);
	}

	init_feature(f_cvc_active, "active", f_type_dynamic);
	// The dependency below may become useful if we use dynamic atom groups
	// f_req_children(f_cvc_active, f_ag_active);

	init_feature(f_cvc_scalar, "scalar", f_type_static);

	init_feature(f_cvc_gradient, "gradient", f_type_dynamic);

	init_feature(f_cvc_implicit_gradient, "implicit gradient", f_type_static);
	f_req_children(f_cvc_implicit_gradient, f_ag_implicit_gradient);

	init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic);
	f_req_self(f_cvc_inv_gradient, f_cvc_gradient);

	init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user);
	f_req_self(f_cvc_debug_gradient, f_cvc_gradient);
	f_req_exclude(f_cvc_debug_gradient, f_cvc_implicit_gradient);

	init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
	f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient);

	init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);

	// init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user);

	// Compute total force on first site only to avoid unwanted
	// coupling to other colvars (see e.g. Ciccotti et al., 2005)
	init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user);
	f_req_self(f_cvc_one_site_total_force, f_cvc_com_based);

	init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
	f_req_self(f_cvc_scalable, f_cvc_scalable_com);

	init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static);
	f_req_self(f_cvc_scalable_com, f_cvc_com_based);


	// TODO only enable this when f_ag_scalable can be turned on for a pre-initialized group
	// f_req_children(f_cvc_scalable, f_ag_scalable);
	// f_req_children(f_cvc_scalable_com, f_ag_scalable_com);
	}

	// Initialize feature_states for each instance
	// default as available, not enabled
	// except dynamic features which default as unavailable
	feature_states.reserve(f_cvc_ntot);
	for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
	bool avail = is_dynamic(i) ? false : true;
	feature_states.push_back(feature_state(avail, false));
	}

	// CVCs are enabled from the start - get disabled based on flags
	feature_states[f_cvc_active].enabled = true;

	// Features that are implemented by all cvcs by default
	// Each cvc specifies what other features are available
	feature_states[f_cvc_active].available = true;
	feature_states[f_cvc_gradient].available = true;

	// Use minimum-image distances by default
	feature_states[f_cvc_pbc_minimum_image].enabled = true;

	// Features that are implemented by default if their requirements are
	feature_states[f_cvc_one_site_total_force].available = true;

	// Features That are implemented only for certain simulation engine configurations
	feature_states[f_cvc_scalable_com].available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
	feature_states[f_cvc_scalable].available = feature_states[f_cvc_scalable_com].available;
	}


	void colvardeps::init_ag_requires() {
	size_t i;
	// Initialize static array once and for all
	if (features().size() == 0) {
	for (i = 0; i < f_ag_ntot; i++) {
	modify_features().push_back(new feature);
	}

	init_feature(f_ag_active, "active", f_type_dynamic);
	init_feature(f_ag_center, "translational fit", f_type_static);
	init_feature(f_ag_rotate, "rotational fit", f_type_static);
	init_feature(f_ag_fitting_group, "reference positions group", f_type_static);
	init_feature(f_ag_implicit_gradient, "implicit atom gradient", f_type_dynamic);
	init_feature(f_ag_fit_gradients, "fit gradients", f_type_user);
	f_req_exclude(f_ag_fit_gradients, f_ag_implicit_gradient);

	init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic);

	// parallel calculation implies that we have at least a scalable center of mass,
	// but f_ag_scalable is kept as a separate feature to deal with future dependencies
	init_feature(f_ag_scalable, "scalable group calculation", f_type_static);
	init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static);
	f_req_self(f_ag_scalable, f_ag_scalable_com);

	// init_feature(f_ag_min_msd_fit, "minimum MSD fit")
	// f_req_self(f_ag_min_msd_fit, f_ag_center)
	// f_req_self(f_ag_min_msd_fit, f_ag_rotate)
	// f_req_exclude(f_ag_min_msd_fit, f_ag_fitting_group)
	}

	// Initialize feature_states for each instance
	// default as unavailable, not enabled
	feature_states.reserve(f_ag_ntot);
	for (i = 0; i < colvardeps::f_ag_ntot; i++) {
	feature_states.push_back(feature_state(false, false));
	}

	// Features that are implemented (or not) by all atom groups
	feature_states[f_ag_active].available = true;
	// f_ag_scalable_com is provided by the CVC iff it is COM-based
	feature_states[f_ag_scalable_com].available = false;
	// TODO make f_ag_scalable depend on f_ag_scalable_com (or something else)
	feature_states[f_ag_scalable].available = true;
	feature_states[f_ag_fit_gradients].available = true;
	feature_states[f_ag_implicit_gradient].available = true;
	}


	void colvardeps::print_state() {
	size_t i;
	cvm::log("Enabled features of \"" + description + "\" (with reference count)");
	for (i = 0; i < feature_states.size(); i++) {
	if (is_enabled(i))
	cvm::log("- " + features()[i]->description + " ("
	+ cvm::to_str(feature_states[i].ref_count) + ")");
	}
	cvm::increase_depth();
	for (i=0; i<children.size(); i++) {
	cvm::log("* child " + cvm::to_str(i+1));
	children[i]->print_state();
	}
	cvm::decrease_depth();
	}



	void colvardeps::add_child(colvardeps *child) {

	children.push_back(child);
	child->parents.push_back((colvardeps *)this);

	// Solve dependencies of already enabled parent features
	// in the new child

	size_t i, fid;
	cvm::increase_depth();
	for (fid = 0; fid < feature_states.size(); fid++) {
	if (is_enabled(fid)) {
	for (i=0; i<features()[fid]->requires_children.size(); i++) {
	int g = features()[fid]->requires_children[i];
	if (cvm::debug()) cvm::log("DEPS: re-enabling children's "
	+ child->features()[g]->description);
	child->enable(g, false, false);
	}
	}
	}
	cvm::decrease_depth();
	}


	void colvardeps::remove_child(colvardeps *child) {
	int i;
	bool found = false;

	for (i = children.size()-1; i>=0; --i) {
	if (children[i] == child) {
	children.erase(children.begin() + i);
	found = true;
	break;
	}
	}
	if (!found) {
	cvm::error("Trying to remove missing child reference from " + description + "\n");
	}
	found = false;
	for (i = child->parents.size()-1; i>=0; --i) {
	if (child->parents[i] == this) {
	child->parents.erase(child->parents.begin() + i);
	found = true;
	break;
	}
	}
	if (!found) {
	cvm::error("Trying to remove missing parent reference from " + child->description + "\n");
	}
	}


	void colvardeps::remove_all_children() {
	size_t i;
	int j;
	bool found;

	for (i = 0; i < children.size(); ++i) {
	found = false;
	for (j = children[i]->parents.size()-1; j>=0; --j) {
	if (children[i]->parents[j] == this) {
	children[i]->parents.erase(children[i]->parents.begin() + j);
	found = true;
	break;
	}
	}
	if (!found) {
	cvm::error("Trying to remove missing parent reference from " + children[i]->description + "\n");
	}
	}
	children.clear();
	}

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