forked from lijiext/lammps
549 lines
18 KiB
C++
549 lines
18 KiB
C++
// -*- c++ -*-
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// This file is part of the Collective Variables module (Colvars).
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// The original version of Colvars and its updates are located at:
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// https://github.com/colvars/colvars
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// Please update all Colvars source files before making any changes.
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// If you wish to distribute your changes, please submit them to the
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// Colvars repository at GitHub.
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#include <algorithm>
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#include "colvarmodule.h"
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#include "colvarvalue.h"
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#include "colvar.h"
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#include "colvarcomp.h"
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colvar::cvc::cvc()
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: sup_coeff(1.0),
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sup_np(1),
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b_periodic(false),
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b_try_scalable(true)
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{
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description = "uninitialized colvar component";
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init_dependencies();
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sup_coeff = 1.0;
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period = 0.0;
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wrap_center = 0.0;
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}
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colvar::cvc::cvc(std::string const &conf)
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: sup_coeff(1.0),
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sup_np(1),
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b_periodic(false),
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b_try_scalable(true)
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{
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description = "uninitialized colvar component";
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init_dependencies();
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sup_coeff = 1.0;
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period = 0.0;
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wrap_center = 0.0;
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init(conf);
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}
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int colvar::cvc::init(std::string const &conf)
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{
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if (cvm::debug())
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cvm::log("Initializing cvc base object.\n");
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std::string const old_name(name);
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if (name.size() > 0) {
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cvm::log("Updating configuration for component \""+name+"\"");
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}
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if (get_keyval(conf, "name", name, name)) {
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if (name.size() > 0) {
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description = "cvc \"" + name + "\" of type " + function_type;
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} else {
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description = "unnamed cvc";
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}
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if ((name != old_name) && (old_name.size() > 0)) {
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cvm::error("Error: cannot rename component \""+old_name+
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"\" after initialization (new name = \""+name+"\")",
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INPUT_ERROR);
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name = old_name;
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}
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}
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get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff);
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get_keyval(conf, "componentExp", sup_np, sup_np);
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get_keyval(conf, "period", period, period);
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get_keyval(conf, "wrapAround", wrap_center, wrap_center);
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get_keyval_feature(dynamic_cast<colvarparse *>(this), conf, "debugGradients",
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f_cvc_debug_gradient, false, parse_silent);
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bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default
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get_keyval(conf, "forceNoPBC", b_no_PBC, b_no_PBC);
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if (b_no_PBC) {
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disable(f_cvc_pbc_minimum_image);
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} else {
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enable(f_cvc_pbc_minimum_image);
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}
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// Attempt scalable calculations when in parallel? (By default yes, if available)
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get_keyval(conf, "scalable", b_try_scalable, b_try_scalable);
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if (cvm::debug())
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cvm::log("Done initializing cvc base object.\n");
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return cvm::get_error();
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}
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int colvar::cvc::init_total_force_params(std::string const &conf)
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{
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if (cvm::get_error()) return COLVARS_ERROR;
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if (get_keyval_feature(this, conf, "oneSiteSystemForce",
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f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
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cvm::log("Warning: keyword \"oneSiteSystemForce\" is deprecated: "
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"please use \"oneSiteTotalForce\" instead.\n");
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}
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if (get_keyval_feature(this, conf, "oneSiteTotalForce",
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f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
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cvm::log("Computing total force on group 1 only");
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}
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if (! is_enabled(f_cvc_one_site_total_force)) {
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// check whether any of the other atom groups is dummy
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std::vector<cvm::atom_group *>::iterator agi = atom_groups.begin();
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agi++;
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for ( ; agi != atom_groups.end(); agi++) {
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if ((*agi)->b_dummy) {
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provide(f_cvc_inv_gradient, false);
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provide(f_cvc_Jacobian, false);
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}
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}
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}
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return COLVARS_OK;
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}
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cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
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char const *group_key,
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bool optional)
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{
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cvm::atom_group *group = NULL;
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std::string group_conf;
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if (key_lookup(conf, group_key, &group_conf)) {
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group = new cvm::atom_group(group_key);
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if (b_try_scalable) {
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if (is_available(f_cvc_scalable_com)
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&& is_enabled(f_cvc_com_based)
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&& !is_enabled(f_cvc_debug_gradient)) {
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enable(f_cvc_scalable_com);
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enable(f_cvc_scalable);
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// The CVC makes the feature available;
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// the atom group will enable it unless it needs to compute a rotational fit
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group->provide(f_ag_scalable_com);
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}
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// TODO check for other types of parallelism here
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}
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if (group_conf.size() == 0) {
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cvm::error("Error: atom group \""+group->key+
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"\" is set, but has no definition.\n",
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INPUT_ERROR);
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return group;
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}
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cvm::increase_depth();
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if (group->parse(group_conf) == COLVARS_OK) {
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register_atom_group(group);
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}
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group->check_keywords(group_conf, group_key);
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if (cvm::get_error()) {
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cvm::error("Error parsing definition for atom group \""+
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std::string(group_key)+"\"\n.", INPUT_ERROR);
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}
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cvm::decrease_depth();
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} else {
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if (! optional) {
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cvm::error("Error: definition for atom group \""+
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std::string(group_key)+"\" not found.\n");
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}
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}
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return group;
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}
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int colvar::cvc::init_dependencies() {
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size_t i;
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// Initialize static array once and for all
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if (features().size() == 0) {
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for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
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modify_features().push_back(new feature);
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}
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init_feature(f_cvc_active, "active", f_type_dynamic);
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// The dependency below may become useful if we use dynamic atom groups
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// require_feature_children(f_cvc_active, f_ag_active);
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init_feature(f_cvc_scalar, "scalar", f_type_static);
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init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
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init_feature(f_cvc_explicit_gradient, "explicit gradient", f_type_static);
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require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient);
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init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic);
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require_feature_self(f_cvc_inv_gradient, f_cvc_gradient);
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init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user);
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require_feature_self(f_cvc_debug_gradient, f_cvc_gradient);
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require_feature_self(f_cvc_debug_gradient, f_cvc_explicit_gradient);
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init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
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require_feature_self(f_cvc_Jacobian, f_cvc_inv_gradient);
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init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);
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init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user);
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// Compute total force on first site only to avoid unwanted
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// coupling to other colvars (see e.g. Ciccotti et al., 2005)
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init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user);
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require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based);
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init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
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require_feature_self(f_cvc_scalable, f_cvc_scalable_com);
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init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static);
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require_feature_self(f_cvc_scalable_com, f_cvc_com_based);
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// TODO only enable this when f_ag_scalable can be turned on for a pre-initialized group
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// require_feature_children(f_cvc_scalable, f_ag_scalable);
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// require_feature_children(f_cvc_scalable_com, f_ag_scalable_com);
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// check that everything is initialized
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for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
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if (is_not_set(i)) {
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cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description);
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}
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}
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}
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// Initialize feature_states for each instance
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// default as available, not enabled
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// except dynamic features which default as unavailable
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feature_states.reserve(f_cvc_ntot);
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for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
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bool avail = is_dynamic(i) ? false : true;
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feature_states.push_back(feature_state(avail, false));
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}
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// Features that are implemented by all cvcs by default
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// Each cvc specifies what other features are available
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feature_states[f_cvc_active].available = true;
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feature_states[f_cvc_gradient].available = true;
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// CVCs are enabled from the start - get disabled based on flags
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enable(f_cvc_active);
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// feature_states[f_cvc_active].enabled = true;
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// Explicit gradients are implemented in mosts CVCs. Exceptions must be specified explicitly.
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// feature_states[f_cvc_explicit_gradient].enabled = true;
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enable(f_cvc_explicit_gradient);
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// Use minimum-image distances by default
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// feature_states[f_cvc_pbc_minimum_image].enabled = true;
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enable(f_cvc_pbc_minimum_image);
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// Features that are implemented by default if their requirements are
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feature_states[f_cvc_one_site_total_force].available = true;
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// Features That are implemented only for certain simulation engine configurations
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feature_states[f_cvc_scalable_com].available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
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feature_states[f_cvc_scalable].available = feature_states[f_cvc_scalable_com].available;
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return COLVARS_OK;
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}
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int colvar::cvc::setup()
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{
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description = "cvc " + name;
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return COLVARS_OK;
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}
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colvar::cvc::~cvc()
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{
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free_children_deps();
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remove_all_children();
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for (size_t i = 0; i < atom_groups.size(); i++) {
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if (atom_groups[i] != NULL) delete atom_groups[i];
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}
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}
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void colvar::cvc::read_data()
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{
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size_t ig;
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for (ig = 0; ig < atom_groups.size(); ig++) {
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cvm::atom_group &atoms = *(atom_groups[ig]);
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atoms.reset_atoms_data();
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atoms.read_positions();
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atoms.calc_required_properties();
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// each atom group will take care of its own fitting_group, if defined
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}
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//// Don't try to get atom velocities, as no back-end currently implements it
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// if (tasks[task_output_velocity] && !tasks[task_fdiff_velocity]) {
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// for (i = 0; i < cvcs.size(); i++) {
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// for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
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// cvcs[i]->atom_groups[ig]->read_velocities();
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// }
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// }
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// }
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}
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std::vector<std::vector<int> > colvar::cvc::get_atom_lists()
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{
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std::vector<std::vector<int> > lists;
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std::vector<cvm::atom_group *>::iterator agi = atom_groups.begin();
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for ( ; agi != atom_groups.end(); ++agi) {
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(*agi)->create_sorted_ids();
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lists.push_back((*agi)->sorted_ids());
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if ((*agi)->is_enabled(f_ag_fitting_group) && (*agi)->is_enabled(f_ag_fit_gradients)) {
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cvm::atom_group &fg = *((*agi)->fitting_group);
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fg.create_sorted_ids();
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lists.push_back(fg.sorted_ids());
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}
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}
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return lists;
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}
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void colvar::cvc::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
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{
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// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
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cvm::real coeff = sup_coeff * cvm::real(sup_np) *
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cvm::integer_power(value().real_value, sup_np-1);
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for (size_t j = 0; j < atom_groups.size(); j++) {
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cvm::atom_group &ag = *(atom_groups[j]);
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// If necessary, apply inverse rotation to get atomic
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// gradient in the laboratory frame
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if (ag.b_rotate) {
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cvm::rotation const rot_inv = ag.rot.inverse();
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for (size_t k = 0; k < ag.size(); k++) {
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size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
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ag[k].id) - atom_ids.begin();
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atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad);
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}
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} else {
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for (size_t k = 0; k < ag.size(); k++) {
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size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
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ag[k].id) - atom_ids.begin();
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atomic_gradients[a] += coeff * ag[k].grad;
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}
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}
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if (ag.is_enabled(f_ag_fitting_group) && ag.is_enabled(f_ag_fit_gradients)) {
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cvm::atom_group const &fg = *(ag.fitting_group);
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for (size_t k = 0; k < fg.size(); k++) {
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size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
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fg[k].id) - atom_ids.begin();
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// fit gradients are in the unrotated (simulation) frame
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atomic_gradients[a] += coeff * fg.fit_gradients[k];
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}
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}
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}
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}
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void colvar::cvc::calc_force_invgrads()
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{
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cvm::error("Error: calculation of inverse gradients is not implemented "
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"for colvar components of type \""+function_type+"\".\n",
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COLVARS_NOT_IMPLEMENTED);
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}
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void colvar::cvc::calc_Jacobian_derivative()
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{
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cvm::error("Error: calculation of inverse gradients is not implemented "
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"for colvar components of type \""+function_type+"\".\n",
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COLVARS_NOT_IMPLEMENTED);
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}
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void colvar::cvc::calc_fit_gradients()
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{
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for (size_t ig = 0; ig < atom_groups.size(); ig++) {
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atom_groups[ig]->calc_fit_gradients();
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}
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}
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void colvar::cvc::debug_gradients()
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{
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// this function should work for any scalar cvc:
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// the only difference will be the name of the atom group (here, "group")
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// NOTE: this assumes that groups for this cvc are non-overlapping,
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// since atom coordinates are modified only within the current group
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cvm::log("Debugging gradients for " + description);
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for (size_t ig = 0; ig < atom_groups.size(); ig++) {
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cvm::atom_group *group = atom_groups[ig];
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if (group->b_dummy) continue;
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cvm::rotation const rot_0 = group->rot;
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cvm::rotation const rot_inv = group->rot.inverse();
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cvm::real x_0 = x.real_value;
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if ((x.type() == colvarvalue::type_vector) && (x.size() == 1)) x_0 = x[0];
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// cvm::log("gradients = "+cvm::to_str (gradients)+"\n");
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cvm::atom_group *group_for_fit = group->fitting_group ? group->fitting_group : group;
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cvm::atom_pos fit_gradient_sum, gradient_sum;
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// print the values of the fit gradients
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if (group->b_rotate || group->b_center) {
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if (group->is_enabled(f_ag_fit_gradients)) {
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size_t j;
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// fit_gradients are in the simulation frame: we should print them in the rotated frame
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cvm::log("Fit gradients:\n");
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for (j = 0; j < group_for_fit->fit_gradients.size(); j++) {
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cvm::log((group->fitting_group ? std::string("refPosGroup") : group->key) +
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"[" + cvm::to_str(j) + "] = " +
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(group->b_rotate ?
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cvm::to_str(rot_0.rotate(group_for_fit->fit_gradients[j])) :
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cvm::to_str(group_for_fit->fit_gradients[j])));
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}
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}
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}
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// debug the gradients
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for (size_t ia = 0; ia < group->size(); ia++) {
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// tests are best conducted in the unrotated (simulation) frame
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cvm::rvector const atom_grad = (group->b_rotate ?
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rot_inv.rotate((*group)[ia].grad) :
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(*group)[ia].grad);
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gradient_sum += atom_grad;
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for (size_t id = 0; id < 3; id++) {
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// (re)read original positions
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group->read_positions();
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// change one coordinate
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(*group)[ia].pos[id] += cvm::debug_gradients_step_size;
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group->calc_required_properties();
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calc_value();
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cvm::real x_1 = x.real_value;
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if ((x.type() == colvarvalue::type_vector) && (x.size() == 1)) x_1 = x[0];
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cvm::log("Atom "+cvm::to_str(ia)+", component "+cvm::to_str(id)+":\n");
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cvm::log("dx(actual) = "+cvm::to_str(x_1 - x_0,
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21, 14)+"\n");
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cvm::real const dx_pred = (group->fit_gradients.size()) ?
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(cvm::debug_gradients_step_size * (atom_grad[id] + group->fit_gradients[ia][id])) :
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(cvm::debug_gradients_step_size * atom_grad[id]);
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cvm::log("dx(interp) = "+cvm::to_str(dx_pred,
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21, 14)+"\n");
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cvm::log("|dx(actual) - dx(interp)|/|dx(actual)| = "+
|
|
cvm::to_str(cvm::fabs(x_1 - x_0 - dx_pred) /
|
|
cvm::fabs(x_1 - x_0), 12, 5)+"\n");
|
|
}
|
|
}
|
|
|
|
if ((group->is_enabled(f_ag_fit_gradients)) && (group->fitting_group != NULL)) {
|
|
cvm::atom_group *ref_group = group->fitting_group;
|
|
group->read_positions();
|
|
group->calc_required_properties();
|
|
|
|
for (size_t ia = 0; ia < ref_group->size(); ia++) {
|
|
|
|
// fit gradients are in the unrotated (simulation) frame
|
|
cvm::rvector const atom_grad = ref_group->fit_gradients[ia];
|
|
fit_gradient_sum += atom_grad;
|
|
|
|
for (size_t id = 0; id < 3; id++) {
|
|
// (re)read original positions
|
|
group->read_positions();
|
|
ref_group->read_positions();
|
|
// change one coordinate
|
|
(*ref_group)[ia].pos[id] += cvm::debug_gradients_step_size;
|
|
group->calc_required_properties();
|
|
calc_value();
|
|
|
|
cvm::real const x_1 = x.real_value;
|
|
cvm::log("refPosGroup atom "+cvm::to_str(ia)+", component "+cvm::to_str (id)+":\n");
|
|
cvm::log("dx(actual) = "+cvm::to_str (x_1 - x_0,
|
|
21, 14)+"\n");
|
|
|
|
cvm::real const dx_pred = cvm::debug_gradients_step_size * atom_grad[id];
|
|
|
|
cvm::log("dx(interp) = "+cvm::to_str (dx_pred,
|
|
21, 14)+"\n");
|
|
cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
|
|
cvm::to_str(cvm::fabs (x_1 - x_0 - dx_pred) /
|
|
cvm::fabs (x_1 - x_0),
|
|
12, 5)+
|
|
".\n");
|
|
}
|
|
}
|
|
}
|
|
|
|
cvm::log("Gradient sum: " + cvm::to_str(gradient_sum) +
|
|
" Fit gradient sum: " + cvm::to_str(fit_gradient_sum) +
|
|
" Total " + cvm::to_str(gradient_sum + fit_gradient_sum));
|
|
}
|
|
return;
|
|
}
|
|
|
|
|
|
cvm::real colvar::cvc::dist2(colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return x1.dist2(x2);
|
|
}
|
|
|
|
|
|
colvarvalue colvar::cvc::dist2_lgrad(colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return x1.dist2_grad(x2);
|
|
}
|
|
|
|
|
|
colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
|
|
colvarvalue const &x2) const
|
|
{
|
|
return x2.dist2_grad(x1);
|
|
}
|
|
|
|
|
|
void colvar::cvc::wrap(colvarvalue &x_unwrapped) const
|
|
{
|
|
return;
|
|
}
|
|
|
|
|
|
// Static members
|
|
|
|
std::vector<colvardeps::feature *> colvar::cvc::cvc_features;
|