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Update Colvars library to version 2024-06-04

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This commit is contained in:
Giacomo Fiorin
2024-08-06 01:07:43 +02:00
parent 278accd9ea
commit 133dee9ac1
74 changed files with 7343 additions and 4676 deletions
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59
lib/colvars/colvarbias_restraint.cpp
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@ -27,7 +27,10 @@ colvarbias_restraint::colvarbias_restraint(char const *key)
int colvarbias_restraint::init(std::string const &conf)
{
colvarbias::init(conf);
int err = colvarbias::init(conf);
if (err != COLVARS_OK) {
return err;
}
enable(f_cvb_apply_force);
colvarbias_ti::init(conf);
@ -202,6 +205,8 @@ int colvarbias_restraint_moving::init(std::string const &conf)
first_step = cvm::step_absolute();
cvm::log("Initial step for restraint change: " + cvm::to_str(first_step) + "\n");
get_keyval(conf, "targetNumSteps", target_nsteps, target_nsteps);
if (!target_nsteps) {
cvm::error("Error: targetNumSteps must be non-zero.\n", COLVARS_INPUT_ERROR);
@ -232,10 +237,9 @@ std::string const colvarbias_restraint_moving::get_state_params() const
std::ostringstream os;
os.setf(std::ios::scientific, std::ios::floatfield);
if (b_chg_centers || b_chg_force_k) {
// TODO move this
os << "firstStep " << std::setw(cvm::it_width) << first_step << "\n";
if (target_nstages) {
os << "stage " << std::setw(cvm::it_width)
<< stage << "\n";
os << "stage " << std::setw(cvm::it_width) << stage << "\n";
}
}
return os.str();
@ -245,6 +249,12 @@ std::string const colvarbias_restraint_moving::get_state_params() const
int colvarbias_restraint_moving::set_state_params(std::string const &conf)
{
if (b_chg_centers || b_chg_force_k) {
auto first_step_flags = colvarparse::parse_restart;
if (cvm::main()->restart_version_number() > 20230906) {
// Only require the first step when the code could produce it
first_step_flags = colvarparse::parse_restart | colvarparse::parse_required;
}
get_keyval(conf, "firstStep", first_step, first_step, first_step_flags);
if (target_nstages) {
get_keyval(conf, "stage", stage, stage,
colvarparse::parse_restart | colvarparse::parse_required);
@ -837,18 +847,6 @@ int colvarbias_restraint_harmonic::set_state_params(std::string const &conf)
}
std::ostream & colvarbias_restraint_harmonic::write_state_data(std::ostream &os)
{
return colvarbias_ti::write_state_data(os);
}
std::istream & colvarbias_restraint_harmonic::read_state_data(std::istream &is)
{
return colvarbias_ti::read_state_data(is);
}
std::ostream & colvarbias_restraint_harmonic::write_traj_label(std::ostream &os)
{
colvarbias_restraint::write_traj_label(os);
@ -1136,18 +1134,6 @@ int colvarbias_restraint_harmonic_walls::set_state_params(std::string const &con
}
std::ostream & colvarbias_restraint_harmonic_walls::write_state_data(std::ostream &os)
{
return colvarbias_ti::write_state_data(os);
}
std::istream & colvarbias_restraint_harmonic_walls::read_state_data(std::istream &is)
{
return colvarbias_ti::read_state_data(is);
}
std::ostream & colvarbias_restraint_harmonic_walls::write_traj_label(std::ostream &os)
{
colvarbias_restraint::write_traj_label(os);
@ -1293,18 +1279,6 @@ int colvarbias_restraint_linear::set_state_params(std::string const &conf)
}
std::ostream & colvarbias_restraint_linear::write_state_data(std::ostream &os)
{
return colvarbias_ti::write_state_data(os);
}
std::istream & colvarbias_restraint_linear::read_state_data(std::istream &is)
{
return colvarbias_ti::read_state_data(is);
}
std::ostream & colvarbias_restraint_linear::write_traj_label(std::ostream &os)
{
colvarbias_restraint::write_traj_label(os);
@ -1338,7 +1312,10 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
{
int error_code = COLVARS_OK;
colvarbias::init(conf);
int err = colvarbias::init(conf);
if (err != COLVARS_OK) {
return err;
}
enable(f_cvb_apply_force);
cvm::main()->cite_feature("histogramRestraint colvar bias implementation");