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Update Colvars library to version 2020-01-27

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One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
This commit is contained in:
Giacomo Fiorin
2020-01-27 13:39:58 -05:00
parent 5eef3b1828
commit 9427fc50a5
56 changed files with 1876 additions and 1017 deletions
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117
lib/colvars/colvarcomp.cpp
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@ -2,7 +2,7 @@
// 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
// 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.
@ -17,30 +17,28 @@
colvar::cvc::cvc()
: sup_coeff(1.0),
sup_np(1),
b_periodic(false),
b_try_scalable(true)
{
description = "uninitialized colvar component";
init_dependencies();
b_try_scalable = true;
sup_coeff = 1.0;
sup_np = 1;
period = 0.0;
wrap_center = 0.0;
width = 0.0;
init_dependencies();
}
colvar::cvc::cvc(std::string const &conf)
: sup_coeff(1.0),
sup_np(1),
b_periodic(false),
b_try_scalable(true)
{
description = "uninitialized colvar component";
init_dependencies();
b_try_scalable = true;
sup_coeff = 1.0;
sup_np = 1;
period = 0.0;
wrap_center = 0.0;
width = 0.0;
init_dependencies();
init(conf);
}
@ -72,11 +70,17 @@ int colvar::cvc::init(std::string const &conf)
get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff);
get_keyval(conf, "componentExp", sup_np, sup_np);
// TODO these could be condensed into get_keyval()
register_param("componentCoeff", reinterpret_cast<void *>(&sup_coeff));
register_param("componentExp", reinterpret_cast<void *>(&sup_np));
get_keyval(conf, "period", period, period);
get_keyval(conf, "wrapAround", wrap_center, wrap_center);
// TODO when init() is called after all constructors, check periodic flag
register_param("period", reinterpret_cast<void *>(&period));
register_param("wrapAround", reinterpret_cast<void *>(&wrap_center));
get_keyval_feature(dynamic_cast<colvarparse *>(this), conf, "debugGradients",
get_keyval_feature(this, conf, "debugGradients",
f_cvc_debug_gradient, false, parse_silent);
bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default
@ -194,6 +198,14 @@ int colvar::cvc::init_dependencies() {
init_feature(f_cvc_scalar, "scalar", f_type_static);
init_feature(f_cvc_periodic, "periodic", f_type_static);
init_feature(f_cvc_width, "defined width", f_type_static);
init_feature(f_cvc_lower_boundary, "defined lower boundary", f_type_static);
init_feature(f_cvc_upper_boundary, "defined upper boundary", f_type_static);
init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
init_feature(f_cvc_explicit_gradient, "explicit gradient", f_type_static);
@ -209,15 +221,15 @@ int colvar::cvc::init_dependencies() {
init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
require_feature_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);
require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based);
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);
init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
require_feature_self(f_cvc_scalable, f_cvc_scalable_com);
@ -291,6 +303,77 @@ colvar::cvc::~cvc()
}
void colvar::cvc::init_as_distance()
{
x.type(colvarvalue::type_scalar);
enable(f_cvc_lower_boundary);
lower_boundary.type(colvarvalue::type_scalar);
lower_boundary.real_value = 0.0;
register_param("lowerBoundary", reinterpret_cast<void *>(&lower_boundary));
}
void colvar::cvc::init_as_angle()
{
x.type(colvarvalue::type_scalar);
init_scalar_boundaries(0.0, 180);
}
void colvar::cvc::init_scalar_boundaries(cvm::real lb, cvm::real ub)
{
enable(f_cvc_lower_boundary);
lower_boundary.type(colvarvalue::type_scalar);
lower_boundary.real_value = lb;
enable(f_cvc_upper_boundary);
upper_boundary.type(colvarvalue::type_scalar);
upper_boundary.real_value = ub;
register_param("lowerBoundary", reinterpret_cast<void *>(&lower_boundary));
register_param("upperBoundary", reinterpret_cast<void *>(&upper_boundary));
}
void colvar::cvc::register_atom_group(cvm::atom_group *ag)
{
atom_groups.push_back(ag);
add_child(ag);
}
colvarvalue const *colvar::cvc::get_param_grad(std::string const &param_name)
{
colvarvalue const *ptr =
reinterpret_cast<colvarvalue const *>(get_param_grad_ptr(param_name));
return ptr != NULL ? ptr : NULL;
}
int colvar::cvc::set_param(std::string const &param_name,
void const *new_value)
{
if (param_map.count(param_name) > 0) {
// TODO When we can use C++11, make this a proper function map
if (param_name.compare("componentCoeff") == 0) {
sup_coeff = *(reinterpret_cast<cvm::real const *>(new_value));
}
if (param_name.compare("componentExp") == 0) {
sup_np = *(reinterpret_cast<int const *>(new_value));
}
if (is_enabled(f_cvc_periodic)) {
if (param_name.compare("period") == 0) {
period = *(reinterpret_cast<cvm::real const *>(new_value));
}
if (param_name.compare("wrapAround") == 0) {
wrap_center = *(reinterpret_cast<cvm::real const *>(new_value));
}
}
}
return colvarparams::set_param(param_name, new_value);
}
void colvar::cvc::read_data()
{
size_t ig;
@ -537,7 +620,7 @@ colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
}
void colvar::cvc::wrap(colvarvalue &x_unwrapped) const
void colvar::cvc::wrap(colvarvalue & /* x_unwrapped */) const
{
return;
}