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lammps/lib/colvars/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_type_dynamic);
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_time_dependent, "time-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);
init_feature(f_cvb_calc_ti_samples, "calculate TI samples", f_type_dynamic);
f_req_self(f_cvb_calc_ti_samples, f_cvb_get_total_force);
f_req_children(f_cvb_calc_ti_samples, f_cv_grid);
init_feature(f_cvb_write_ti_samples, "write TI samples ", f_type_user);
f_req_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples);
init_feature(f_cvb_write_ti_pmf, "write TI PMF", f_type_user);
f_req_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples);
}
// 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
}
// only compute TI samples when deriving from colvarbias_ti
feature_states[f_cvb_calc_ti_samples].available = false;
}
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);
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_dynamic);
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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