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Update Colvars to version 2020-09-17

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Small changes

Implement global map of components (@HanatoK)
https://github.com/Colvars/colvars/pull/363

Format code examples with colored background (@giacomofiorin)
https://github.com/Colvars/colvars/pull/361

replaced jacobi() with an open-source version (@jewettaij)
https://github.com/Colvars/colvars/pull/360
This commit is contained in:
Giacomo Fiorin
2020-09-18 16:54:32 -04:00
parent 34ba8ec83c
commit 7deb773440
10 changed files with 405 additions and 276 deletions
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39
lib/colvars/colvarcomp_gpath.cpp
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@ -19,10 +19,6 @@
#include "colvar.h"
#include "colvarcomp.h"
namespace GeometricPathCV {
void init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& conf)>>& string_cv_map);
}
bool compareColvarComponent(colvar::cvc *i, colvar::cvc *j)
{
return i->name < j->name;
@ -406,9 +402,8 @@ void colvar::gzpath::apply_force(colvarvalue const &force) {
}
colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) {
GeometricPathCV::init_string_cv_map(string_cv_map);
// Lookup all available sub-cvcs
for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
for (auto it_cv_map = colvar::get_global_cvc_map().begin(); it_cv_map != colvar::get_global_cvc_map().end(); ++it_cv_map) {
if (key_lookup(conf, it_cv_map->first.c_str())) {
std::vector<std::string> sub_cvc_confs;
get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
@ -506,9 +501,8 @@ void colvar::linearCombination::apply_force(colvarvalue const &force) {
}
colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
GeometricPathCV::init_string_cv_map(string_cv_map);
// Lookup all available sub-cvcs
for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
for (auto it_cv_map = colvar::get_global_cvc_map().begin(); it_cv_map != colvar::get_global_cvc_map().end(); ++it_cv_map) {
if (key_lookup(conf, it_cv_map->first.c_str())) {
std::vector<std::string> sub_cvc_confs;
get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
@ -909,33 +903,4 @@ void colvar::gzpathCV::apply_force(colvarvalue const &force) {
}
}
void GeometricPathCV::init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& string_cv_map) {
string_cv_map["distance"] = [](const std::string& conf){return new colvar::distance(conf);};
string_cv_map["dihedral"] = [](const std::string& conf){return new colvar::dihedral(conf);};
string_cv_map["angle"] = [](const std::string& conf){return new colvar::angle(conf);};
string_cv_map["rmsd"] = [](const std::string& conf){return new colvar::rmsd(conf);};
string_cv_map["gyration"] = [](const std::string& conf){return new colvar::gyration(conf);};
string_cv_map["inertia"] = [](const std::string& conf){return new colvar::inertia(conf);};
string_cv_map["inertiaZ"] = [](const std::string& conf){return new colvar::inertia_z(conf);};
string_cv_map["tilt"] = [](const std::string& conf){return new colvar::tilt(conf);};
string_cv_map["distanceZ"] = [](const std::string& conf){return new colvar::distance_z(conf);};
string_cv_map["distanceXY"] = [](const std::string& conf){return new colvar::distance_xy(conf);};
string_cv_map["polarTheta"] = [](const std::string& conf){return new colvar::polar_theta(conf);};
string_cv_map["polarPhi"] = [](const std::string& conf){return new colvar::polar_phi(conf);};
string_cv_map["distanceVec"] = [](const std::string& conf){return new colvar::distance_vec(conf);};
string_cv_map["orientationAngle"] = [](const std::string& conf){return new colvar::orientation_angle(conf);};
string_cv_map["distancePairs"] = [](const std::string& conf){return new colvar::distance_pairs(conf);};
string_cv_map["dipoleMagnitude"] = [](const std::string& conf){return new colvar::dipole_magnitude(conf);};
string_cv_map["coordNum"] = [](const std::string& conf){return new colvar::coordnum(conf);};
string_cv_map["selfCoordNum"] = [](const std::string& conf){return new colvar::selfcoordnum(conf);};
string_cv_map["dipoleAngle"] = [](const std::string& conf){return new colvar::dipole_angle(conf);};
string_cv_map["orientation"] = [](const std::string& conf){return new colvar::orientation(conf);};
string_cv_map["orientationProj"] = [](const std::string& conf){return new colvar::orientation_proj(conf);};
string_cv_map["eigenvector"] = [](const std::string& conf){return new colvar::eigenvector(conf);};
string_cv_map["cartesian"] = [](const std::string& conf){return new colvar::cartesian(conf);};
string_cv_map["alpha"] = [](const std::string& conf){return new colvar::alpha_angles(conf);};
string_cv_map["dihedralPC"] = [](const std::string& conf){return new colvar::dihedPC(conf);};
string_cv_map["linearCombination"] = [](const std::string& conf){return new colvar::linearCombination(conf);};
}
#endif