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Update Colvars library to version 2016-12-22

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Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
This commit is contained in:
Giacomo Fiorin
2016-12-27 13:17:34 -05:00
parent 6ab716164b
commit f553e230db
49 changed files with 2489 additions and 1358 deletions
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22
lib/colvars/colvardeps.cpp
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@ -1,3 +1,13 @@
// -*- 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"
@ -219,6 +229,9 @@ void colvardeps::init_cvb_requires() {
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++) {
@ -229,6 +242,9 @@ void colvardeps::init_cvb_requires() {
// 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;
}
@ -321,6 +337,7 @@ void colvardeps::init_cv_requires() {
// 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");
@ -407,6 +424,11 @@ void colvardeps::init_cvc_requires() {
// 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;
}