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update colvars library to version 2016-09-30

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This commit is contained in:
Axel Kohlmeyer
2016-09-30 08:15:44 -04:00
parent f7b5afee82
commit 6d200061ca
20 changed files with 728 additions and 155 deletions
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54
lib/colvars/colvar.cpp
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@ -150,7 +150,7 @@ colvar::colvar(std::string const &conf)
feature_states[f_cv_linear]->enabled = lin;
}
// Colvar is homogeneous iff:
// Colvar is homogeneous if:
// - it is linear (hence not scripted)
// - all cvcs have coefficient 1 or -1
// i.e. sum or difference of cvcs
@ -375,28 +375,16 @@ colvar::colvar(std::string const &conf)
{
bool temp;
if (get_keyval(conf, "outputSystemForce", temp, false)) {
cvm::error("Colvar option outputSystemForce is deprecated.\n"
"Please use outputTotalForce, or outputSystemForce within an ABF bias.");
if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) {
cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n"
"The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
return;
}
}
{
bool b_output_total_force;
get_keyval(conf, "outputTotalForce", b_output_total_force, false);
if (b_output_total_force) {
enable(f_cv_output_total_force);
}
}
{
bool b_output_applied_force;
get_keyval(conf, "outputAppliedForce", b_output_applied_force, false);
if (b_output_applied_force) {
enable(f_cv_output_applied_force);
}
}
get_keyval_feature(this, conf, "outputTotalForce", f_cv_output_total_force, false);
get_keyval_feature(this, conf, "outputAppliedForce", f_cv_output_applied_force, false);
get_keyval_feature(this, conf, "subtractAppliedForce", f_cv_subtract_applied_force, false);
// Start in active state by default
enable(f_cv_active);
@ -409,6 +397,8 @@ colvar::colvar(std::string const &conf)
fj.type(value());
ft.type(value());
ft_reported.type(value());
f_old.type(value());
f_old.reset();
if (cvm::b_analysis)
parse_analysis(conf);
@ -519,6 +509,8 @@ int colvar::init_components(std::string const &conf)
"number", "coordNum");
error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
"number", "selfCoordNum");
error_code |= init_components_type<groupcoordnum>(conf, "group-coordination "
"number", "groupCoord");
error_code |= init_components_type<angle>(conf, "angle", "angle");
error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral");
@ -1104,6 +1096,14 @@ int colvar::calc_colvar_properties()
} else {
if (is_enabled(f_cv_subtract_applied_force)) {
// correct the total force only if it has been measured
// TODO add a specific test instead of relying on sq norm
if (ft.norm2() > 0.0) {
ft -= f_old;
}
}
x_reported = x;
ft_reported = ft;
}
@ -1210,6 +1210,10 @@ cvm::real colvar::update_forces_energy()
x_old = x;
}
if (is_enabled(f_cv_subtract_applied_force)) {
f_old = f;
}
if (cvm::debug())
cvm::log("Done updating colvar \""+this->name+"\".\n");
return (potential_energy + kinetic_energy);
@ -1640,15 +1644,9 @@ std::ostream & colvar::write_traj(std::ostream &os)
}
if (is_enabled(f_cv_output_applied_force)) {
if (is_enabled(f_cv_extended_Lagrangian)) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< fr;
} else {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< f;
}
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< applied_force();
}
return os;