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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() {
size_t i;
for (i=0; i<feature_states.size(); i++) {
if (feature_states[i] != NULL) delete feature_states[i];
}
// Do not delete features if it's static
// for (i=0; i<features.size(); i++) {
// if (features[i] != NULL) delete features[i];
// }
remove_all_children();
// Protest if we are deleting an object while a parent object may still depend on it
// Another possible strategy is to have the child unlist itself from the parent's children
if (parents.size()) {
cvm::log("Warning: destroying " + description + " before its parents objects:");
for (i=0; i<parents.size(); i++) {
cvm::log(parents[i]->description);
}
}
}
void colvardeps::provide(int feature_id) {
feature_states[feature_id]->available = true;
}
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)
{
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 " : " requiring ") +
"\"" + f->description +"\"");
}
if (fs->enabled) {
// Do not try to solve deps if already enabled
return COLVARS_OK;
}
if (!fs->available) {
if (!dry_run) {
if (toplevel) {
cvm::error("Error: Feature unavailable: \"" + f->description + "\" in " + description + ".");
} else {
cvm::log("Feature unavailable: \"" + f->description + "\" in " + description);
}
}
return COLVARS_ERROR;
}
// 1) enforce exclusions
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("Features \"" + 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
break;
}
}
if (!ok) {
if (!dry_run) {
cvm::log("No dependency satisfied among alternates:");
cvm::log("-----------------------------------------");
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);
cvm::increase_depth();
enable(g, false, false); // Just for printing error output
cvm::decrease_depth();
}
cvm::log("-----------------------------------------");
cvm::log("for \"" + f->description + "\" in " + description);
if (toplevel) {
cvm::error("Error: Failed dependency in " + description + ".");
}
}
return COLVARS_ERROR;
}
}
// 4) solve deps in children
for (i=0; i<f->requires_children.size(); i++) {
int g = f->requires_children[i];
for (j=0; j<children.size(); j++) {
cvm::increase_depth();
res = children[j]->enable(g, dry_run, false);
cvm::decrease_depth();
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;
}
}
// If we've just touched the features of child objects, refresh them
if (!dry_run && f->requires_children.size() != 0) {
for (j=0; j<children.size(); j++) {
children[j]->refresh_deps();
}
}
}
// Actually enable feature only once everything checks out
if (!dry_run) fs->enabled = true;
return COLVARS_OK;
}
// disable() {
//
// // we need refs to parents to walk up the deps tree!
// // or refresh
// }
// Shorthand macros for describing dependencies
#define f_description(f, d) features()[f]->description = d
#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
void colvardeps::init_cvb_requires() {
int i;
if (features().size() == 0) {
for (i = 0; i < f_cvb_ntot; i++) {
features().push_back(new feature);
}
}
f_description(f_cvb_active, "active");
f_req_children(f_cvb_active, f_cv_active);
f_description(f_cvb_apply_force, "apply force");
f_req_children(f_cvb_apply_force, f_cv_gradient);
f_description(f_cvb_get_total_force, "obtain total force");
f_req_children(f_cvb_get_total_force, f_cv_total_force);
f_description(f_cvb_history_dependent, "history-dependent");
f_description(f_cvb_scalar_variables, "require scalar variables");
f_req_children(f_cvb_scalar_variables, f_cv_scalar);
// Initialize feature_states for each instance
feature_states.reserve(f_cvb_ntot);
for (i = 0; i < f_cvb_ntot; i++) {
feature_states.push_back(new feature_state(true, false));
// Most features are available, so we set them so
// and list exceptions below
}
// some biases are not history-dependent
feature_states[f_cvb_history_dependent]->available = false;
// by default, biases should work with vector variables, too
feature_states[f_cvb_scalar_variables]->available = false;
}
void colvardeps::init_cv_requires() {
size_t i;
if (features().size() == 0) {
for (i = 0; i < f_cv_ntot; i++) {
features().push_back(new feature);
}
f_description(f_cv_active, "active");
f_req_children(f_cv_active, f_cvc_active);
// Colvars must be either a linear combination, or scalar (and polynomial) or scripted
f_req_alt3(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted);
f_description(f_cv_gradient, "gradient");
f_req_children(f_cv_gradient, f_cvc_gradient);
f_description(f_cv_collect_gradient, "collect gradient");
f_req_self(f_cv_collect_gradient, f_cv_gradient);
f_req_self(f_cv_collect_gradient, f_cv_scalar);
f_description(f_cv_fdiff_velocity, "fdiff_velocity");
// System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
f_description(f_cv_total_force, "total force");
f_req_alt2(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
// Deps for explicit total force calculation
f_description(f_cv_total_force_calc, "total force calculation");
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);
f_description(f_cv_Jacobian, "Jacobian derivative");
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);
f_description(f_cv_hide_Jacobian, "hide Jacobian force");
f_req_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated
f_description(f_cv_extended_Lagrangian, "extended Lagrangian");
f_description(f_cv_Langevin, "Langevin dynamics");
f_req_self(f_cv_Langevin, f_cv_extended_Lagrangian);
f_description(f_cv_linear, "linear");
f_description(f_cv_scalar, "scalar");
f_description(f_cv_output_energy, "output energy");
f_description(f_cv_output_value, "output value");
f_description(f_cv_output_velocity, "output velocity");
f_req_self(f_cv_output_velocity, f_cv_fdiff_velocity);
f_description(f_cv_output_applied_force, "output applied force");
f_description(f_cv_output_total_force, "output total force");
f_req_self(f_cv_output_total_force, f_cv_total_force);
f_description(f_cv_subtract_applied_force, "subtract applied force from total force");
f_req_self(f_cv_subtract_applied_force, f_cv_total_force);
f_description(f_cv_lower_boundary, "lower boundary");
f_req_self(f_cv_lower_boundary, f_cv_scalar);
f_description(f_cv_upper_boundary, "upper boundary");
f_req_self(f_cv_upper_boundary, f_cv_scalar);
f_description(f_cv_grid, "grid");
f_req_self(f_cv_grid, f_cv_lower_boundary);
f_req_self(f_cv_grid, f_cv_upper_boundary);
f_description(f_cv_lower_wall, "lower wall");
f_req_self(f_cv_lower_wall, f_cv_lower_boundary);
f_req_self(f_cv_lower_wall, f_cv_gradient);
f_description(f_cv_upper_wall, "upper wall");
f_req_self(f_cv_upper_wall, f_cv_upper_boundary);
f_req_self(f_cv_upper_wall, f_cv_gradient);
f_description(f_cv_runave, "running average");
f_description(f_cv_corrfunc, "correlation function");
// The features below are set programmatically
f_description(f_cv_scripted, "scripted");
f_description(f_cv_periodic, "periodic");
f_req_self(f_cv_periodic, f_cv_homogeneous);
f_description(f_cv_scalar, "scalar");
f_description(f_cv_linear, "linear");
f_description(f_cv_homogeneous, "homogeneous");
}
// Initialize feature_states for each instance
feature_states.reserve(f_cv_ntot);
for (i = 0; i < f_cv_ntot; i++) {
feature_states.push_back(new feature_state(true, false));
// Most features are available, so we set them so
// and list exceptions below
}
// properties that may NOT be enabled as a dependency
int unavailable_deps[] = {
f_cv_lower_boundary,
f_cv_upper_boundary,
f_cv_extended_Lagrangian,
f_cv_Langevin,
f_cv_scripted,
f_cv_periodic,
f_cv_scalar,
f_cv_linear,
f_cv_homogeneous
};
for (i = 0; i < sizeof(unavailable_deps) / sizeof(unavailable_deps[0]); i++) {
feature_states[unavailable_deps[i]]->available = false;
}
}
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++) {
features().push_back(new feature);
}
f_description(f_cvc_active, "active");
// The dependency below may become useful if we use dynamic atom groups
// f_req_children(f_cvc_active, f_ag_active);
f_description(f_cvc_scalar, "scalar");
f_description(f_cvc_gradient, "gradient");
f_description(f_cvc_inv_gradient, "inverse gradient");
f_req_self(f_cvc_inv_gradient, f_cvc_gradient);
f_description(f_cvc_debug_gradient, "debug gradient");
f_req_self(f_cvc_debug_gradient, f_cvc_gradient);
f_description(f_cvc_Jacobian, "Jacobian derivative");
f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient);
f_description(f_cvc_com_based, "depends on group centers of mass");
// Compute total force on first site only to avoid unwanted
// coupling to other colvars (see e.g. Ciccotti et al., 2005)
f_description(f_cvc_one_site_total_force, "compute total collective force only from one group center");
f_req_self(f_cvc_one_site_total_force, f_cvc_com_based);
f_description(f_cvc_scalable, "scalable calculation");
f_req_self(f_cvc_scalable, f_cvc_scalable_com);
f_description(f_cvc_scalable_com, "scalable calculation of centers of mass");
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 unavailable, not enabled
feature_states.reserve(f_cvc_ntot);
for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
feature_states.push_back(new feature_state(false, false));
}
// 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;
// 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++) {
features().push_back(new feature);
}
f_description(f_ag_active, "active");
f_description(f_ag_center, "translational fit");
f_description(f_ag_rotate, "rotational fit");
f_description(f_ag_fitting_group, "reference positions group");
f_description(f_ag_fit_gradient_group, "fit gradient for main group");
f_description(f_ag_fit_gradient_ref, "fit gradient for reference group");
f_description(f_ag_atom_forces, "atomic forces");
// 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
f_description(f_ag_scalable, "scalable group calculation");
f_description(f_ag_scalable_com, "scalable group center of mass calculation");
f_req_self(f_ag_scalable, f_ag_scalable_com);
// f_description(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(new 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;
}
void colvardeps::print_state() {
size_t i;
cvm::log("Enabled features of " + description);
for (i = 0; i < feature_states.size(); i++) {
if (feature_states[i]->enabled)
cvm::log("- " + features()[i]->description);
}
for (i=0; i<children.size(); i++) {
cvm::log("* child " + cvm::to_str(i+1));
cvm::increase_depth();
children[i]->print_state();
cvm::decrease_depth();
}
}
void colvardeps::add_child(colvardeps *child) {
children.push_back(child);
child->parents.push_back((colvardeps *)this);
}
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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