colvar::distance_z::distance_z(std::string const &conf)
: cvc(conf)
{
function_type = "distance_z";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
// TODO detect PBC from MD engine (in simple cases)
// and then update period in real time
if (period != 0.0)
b_periodic = true;
if ((wrap_center != 0.0) && (period == 0.0)) {
cvm::error("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
return;
}
main = parse_group(conf, "main");
ref1 = parse_group(conf, "ref");
// this group is optional
ref2 = parse_group(conf, "ref2", true);
if (ref2 && ref2->size()) {
cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
fixed_axis = false;
if (key_lookup(conf, "axis"))
cvm::log("Warning: explicit axis definition will be ignored!");
} else {
if (get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0) {
cvm::error("Axis vector is zero!");
return;
}
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log("The normalized axis is: "+cvm::to_str(axis)+".\n");
}
}
fixed_axis = true;
}
if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log("Computing distance using absolute positions (not minimal-image)");
}
init_total_force_params(conf);
}
colvar::distance::distance(std::string const &conf)
: cvc(conf)
{
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
init_total_force_params(conf);
x.type(colvarvalue::type_scalar);
}
colvar::distance::distance(std::string const &conf)
: cvc(conf)
{
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log("Computing distance using absolute positions (not minimal-image)");
}
init_total_force_params(conf);
x.type(colvarvalue::type_scalar);
}