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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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6
lib/colvars/colvarcomp_protein.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.
@ -30,6 +30,8 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
enable(f_cvc_explicit_gradient);
x.type(colvarvalue::type_scalar);
colvarproxy *proxy = cvm::main()->proxy;
std::string segment_id;
get_keyval(conf, "psfSegID", segment_id, std::string("MAIN"));
@ -91,7 +93,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
{
cvm::real r0;
size_t en, ed;
get_keyval(conf, "hBondCutoff", r0, (3.3 * cvm::unit_angstrom()));
get_keyval(conf, "hBondCutoff", r0, (3.3 * proxy->angstrom_value));
get_keyval(conf, "hBondExpNumer", en, 6);
get_keyval(conf, "hBondExpDenom", ed, 8);