ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Update Colvars to version 2020-02-27

Browse Source 
This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
This commit is contained in:
Giacomo Fiorin
2020-02-27 19:44:33 -05:00
parent 6e7e365981
commit 7be004512f
24 changed files with 508 additions and 365 deletions
Download Patch File Download Diff File Expand all files Collapse all files

83
lib/colvars/colvarbias_restraint.cpp
View File

@ -17,6 +17,7 @@
colvarbias_restraint::colvarbias_restraint(char const *key)
: colvarbias(key), colvarbias_ti(key)
{
state_keyword = "restraint";
}
@ -705,67 +706,6 @@ std::ostream & colvarbias_restraint_k_moving::write_traj(std::ostream &os)
// redefined due to legacy state file keyword "harmonic"
std::istream & colvarbias_restraint::read_state(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, brace, conf;
if ( !(is >> key) || !(key == "restraint" || key == "harmonic") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block("configuration", conf)) ||
(set_state_params(conf) != COLVARS_OK) ) {
cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
this->name+"\" at position "+
cvm::to_str(static_cast<size_t>(is.tellg()))+
" in stream.\n", INPUT_ERROR);
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if (!read_state_data(is)) {
cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+
this->name+"\" at position "+
cvm::to_str(static_cast<size_t>(is.tellg()))+
" in stream.\n", INPUT_ERROR);
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
}
is >> brace;
if (brace != "}") {
cvm::log("brace = "+brace+"\n");
cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str(static_cast<size_t>(is.tellg()))+" in stream.\n");
is.setstate(std::ios::failbit);
}
return is;
}
std::ostream & colvarbias_restraint::write_state(std::ostream &os)
{
os.setf(std::ios::scientific, std::ios::floatfield);
os << "restraint {\n"
<< " configuration {\n";
std::istringstream is(get_state_params());
std::string line;
while (std::getline(is, line)) {
os << " " << line << "\n";
}
os << " }\n";
write_state_data(os);
os << "}\n\n";
return os;
}
colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(char const *key)
: colvarbias(key),
colvarbias_ti(key),
@ -928,6 +868,9 @@ colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char co
{
lower_wall_k = -1.0;
upper_wall_k = -1.0;
// This bias implements the bias_actual_colvars feature (most others do not)
provide(f_cvb_bypass_ext_lagrangian);
set_enabled(f_cvb_bypass_ext_lagrangian); // Defaults to enabled
}
@ -1075,23 +1018,13 @@ int colvarbias_restraint_harmonic_walls::update()
}
void colvarbias_restraint_harmonic_walls::communicate_forces()
{
for (size_t i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("Communicating a force to colvar \""+
variables(i)->name+"\".\n");
}
// Impulse-style multiple timestep
variables(i)->add_bias_force_actual_value(cvm::real(time_step_factor) * colvar_forces[i]);
}
}
cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const
{
colvar *cv = variables(i);
colvarvalue const &cvv = variables(i)->actual_value();
colvarvalue const &cvv = is_enabled(f_cvb_bypass_ext_lagrangian) ?
variables(i)->actual_value() :
variables(i)->value();
// For a periodic colvar, both walls may be applicable at the same time
// in which case we pick the closer one