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update colvars library to latest version

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This commit is contained in:
Axel Kohlmeyer
2012-06-07 19:12:29 -04:00
parent b36b069f3d
commit 13b28920ac
13 changed files with 410 additions and 130 deletions
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16
lib/colvars/colvar.cpp
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@ -22,7 +22,7 @@ colvar::colvar (std::string const &conf)
cvi < cvm::colvars.end();
cvi++) {
if ((*cvi)->name == this->name)
cvm::fatal_error ("Error: this colvar has the same name, \""+this->name+
cvm::fatal_error ("Error: this colvar cannot have the same name, \""+this->name+
"\", as another colvar.\n");
}
@ -98,7 +98,8 @@ colvar::colvar (std::string const &conf)
"on an axis", "distanceZ", distance_z);
initialize_components ("distance projection "
"on a plane", "distanceXY", distance_xy);
initialize_components ("minimum distance", "minDistance", min_distance);
initialize_components ("average distance weighted by inverse sixth power",
"distance6", distance6);
initialize_components ("coordination "
"number", "coordNum", coordnum);
@ -128,6 +129,10 @@ colvar::colvar (std::string const &conf)
initialize_components ("radius of "
"gyration", "gyration", gyration);
initialize_components ("moment of "
"inertia", "inertia", inertia);
initialize_components ("moment of inertia around an axis",
"inertia_z", inertia_z);
initialize_components ("eigenvector", "eigenvector", eigenvector);
if (!cvcs.size())
@ -249,6 +254,13 @@ colvar::colvar (std::string const &conf)
}
}
if (tasks[task_lower_boundary]) {
get_keyval (conf, "hardLowerBoundary", hard_lower_boundary, false);
}
if (tasks[task_upper_boundary]) {
get_keyval (conf, "hardUpperBoundary", hard_upper_boundary, false);
}
// consistency checks for boundaries and walls
if (tasks[task_lower_boundary] && tasks[task_upper_boundary]) {
if (lower_boundary >= upper_boundary) {