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Update Colvars to version 2017-07-15 and support automated builds for it

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This commit is contained in:
Giacomo Fiorin
2017-07-19 14:10:43 -04:00
parent cc9b3864bf
commit ee6cac826e
52 changed files with 3473 additions and 2413 deletions
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14
lib/colvars/colvarcomp_rotations.cpp
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@ -22,6 +22,7 @@ colvar::orientation::orientation(std::string const &conf)
{
function_type = "orientation";
atoms = parse_group(conf, "atoms");
enable(f_cvc_implicit_gradient);
x.type(colvarvalue::type_quaternion);
ref_pos.reserve(atoms->size());
@ -29,8 +30,9 @@ colvar::orientation::orientation(std::string const &conf)
if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) {
cvm::log("Using reference positions from input file.\n");
if (ref_pos.size() != atoms->size()) {
cvm::fatal_error("Error: reference positions do not "
cvm::error("Error: reference positions do not "
"match the number of requested atoms.\n");
return;
}
}
@ -43,9 +45,11 @@ colvar::orientation::orientation(std::string const &conf)
if (get_keyval(conf, "refPositionsCol", file_col, std::string(""))) {
// use PDB flags if column is provided
bool found = get_keyval(conf, "refPositionsColValue", file_col_value, 0.0);
if (found && file_col_value==0.0)
cvm::fatal_error("Error: refPositionsColValue, "
if (found && file_col_value==0.0) {
cvm::error("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
}
} else {
// if not, use atom indices
atoms->create_sorted_ids();
@ -56,8 +60,9 @@ colvar::orientation::orientation(std::string const &conf)
}
if (!ref_pos.size()) {
cvm::fatal_error("Error: must define a set of "
cvm::error("Error: must define a set of "
"reference coordinates.\n");
return;
}
@ -88,6 +93,7 @@ colvar::orientation::orientation()
: cvc()
{
function_type = "orientation";
enable(f_cvc_implicit_gradient);
x.type(colvarvalue::type_quaternion);
}