update colvars to version 2016-08-10
This commit is contained in:
Axel Kohlmeyer
@ -43,7 +43,8 @@ colvar::colvar(std::string const &conf)
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kinetic_energy = 0.0;
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potential_energy = 0.0;
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cvm::combine_errors(error_code, init_components(conf));
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error_code |= init_components(conf);
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if (error_code != COLVARS_OK) return;
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size_t i;
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@ -492,110 +493,44 @@ int colvar::init_components(std::string const &conf)
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{
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int error_code = COLVARS_OK;
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cvm::combine_errors(error_code,
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init_components_type<distance>(conf,
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"distance", "distance"));
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cvm::combine_errors(error_code,
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init_components_type<distance_vec>(conf,
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"distance vector", "distanceVec"));
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cvm::combine_errors(error_code,
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init_components_type<cartesian>(conf,
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"Cartesian coordinates", "cartesian"));
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cvm::combine_errors(error_code,
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init_components_type<distance_dir>(conf,
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"distance vector "
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"direction", "distanceDir"));
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cvm::combine_errors(error_code,
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init_components_type<distance_z>(conf,
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"distance projection "
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"on an axis", "distanceZ"));
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cvm::combine_errors(error_code,
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init_components_type<distance_xy>(conf,
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"distance projection "
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"on a plane", "distanceXY"));
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cvm::combine_errors(error_code,
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init_components_type<distance_inv>(conf,
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"average distance "
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"weighted by inverse power",
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"distanceInv"));
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cvm::combine_errors(error_code,
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init_components_type<distance_pairs>(conf,
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"N1xN2-long vector "
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"of pairwise distances",
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"distancePairs"));
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cvm::combine_errors(error_code,
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init_components_type<coordnum>(conf,
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"coordination "
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"number", "coordNum"));
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cvm::combine_errors(error_code,
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init_components_type<selfcoordnum>(conf,
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"self-coordination "
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"number", "selfCoordNum"));
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cvm::combine_errors(error_code,
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init_components_type<angle>(conf,
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"angle", "angle"));
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cvm::combine_errors(error_code,
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init_components_type<dipole_angle>(conf,
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"dipole angle", "dipoleAngle"));
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cvm::combine_errors(error_code,
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init_components_type<dihedral>(conf,
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"dihedral", "dihedral"));
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cvm::combine_errors(error_code,
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init_components_type<h_bond>(conf,
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"hydrogen bond", "hBond"));
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// cvm::combine_errors(error_code, init_components_type<alpha_dihedrals>(conf, "alpha helix", "alphaDihedrals"));
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cvm::combine_errors(error_code,
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init_components_type<alpha_angles>(conf,
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"alpha helix", "alpha"));
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cvm::combine_errors(error_code,
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init_components_type<dihedPC>(conf,
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"dihedral "
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"principal component", "dihedralPC"));
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cvm::combine_errors(error_code,
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init_components_type<orientation>(conf,
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"orientation", "orientation"));
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cvm::combine_errors(error_code,
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init_components_type<orientation_angle>(conf,
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"orientation "
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"angle", "orientationAngle"));
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cvm::combine_errors(error_code,
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init_components_type<orientation_proj>(conf,
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"orientation "
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"projection", "orientationProj"));
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cvm::combine_errors(error_code,
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init_components_type<tilt>(conf,
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"tilt", "tilt"));
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cvm::combine_errors(error_code,
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init_components_type<spin_angle>(conf,
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"spin angle", "spinAngle"));
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cvm::combine_errors(error_code,
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init_components_type<rmsd>(conf,
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"RMSD", "rmsd"));
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// cvm::combine_errors(error_code, init_components_type <logmsd>(conf,"logarithm of MSD", "logmsd"));
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cvm::combine_errors(error_code,
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init_components_type<gyration>(conf,
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"radius of "
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"gyration", "gyration"));
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cvm::combine_errors(error_code,
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init_components_type<inertia>(conf,
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"moment of "
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"inertia", "inertia"));
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cvm::combine_errors(error_code,
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init_components_type<inertia_z>(conf,
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"moment of inertia around an axis",
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"inertiaZ"));
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cvm::combine_errors(error_code,
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init_components_type<eigenvector>(conf,
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"eigenvector", "eigenvector"));
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error_code |= init_components_type<distance>(conf, "distance", "distance");
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error_code |= init_components_type<distance_vec>(conf, "distance vector", "distanceVec");
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error_code |= init_components_type<cartesian>(conf, "Cartesian coordinates", "cartesian");
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error_code |= init_components_type<distance_dir>(conf, "distance vector "
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"direction", "distanceDir");
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error_code |= init_components_type<distance_z>(conf, "distance projection "
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"on an axis", "distanceZ");
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error_code |= init_components_type<distance_xy>(conf, "distance projection "
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"on a plane", "distanceXY");
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error_code |= init_components_type<distance_inv>(conf, "average distance "
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"weighted by inverse power", "distanceInv");
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error_code |= init_components_type<distance_pairs>(conf, "N1xN2-long vector "
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"of pairwise distances", "distancePairs");
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error_code |= init_components_type<coordnum>(conf, "coordination "
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"number", "coordNum");
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error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
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"number", "selfCoordNum");
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error_code |= init_components_type<angle>(conf, "angle", "angle");
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error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
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error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral");
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error_code |= init_components_type<h_bond>(conf, "hydrogen bond", "hBond");
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error_code |= init_components_type<alpha_angles>(conf, "alpha helix", "alpha");
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error_code |= init_components_type<dihedPC>(conf, "dihedral "
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"principal component", "dihedralPC");
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error_code |= init_components_type<orientation>(conf, "orientation", "orientation");
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error_code |= init_components_type<orientation_angle>(conf, "orientation "
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"angle", "orientationAngle");
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error_code |= init_components_type<orientation_proj>(conf, "orientation "
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"projection", "orientationProj");
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error_code |= init_components_type<tilt>(conf, "tilt", "tilt");
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error_code |= init_components_type<spin_angle>(conf, "spin angle", "spinAngle");
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error_code |= init_components_type<rmsd>(conf, "RMSD", "rmsd");
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error_code |= init_components_type<gyration>(conf, "radius of "
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"gyration", "gyration");
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error_code |= init_components_type<inertia>(conf, "moment of "
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"inertia", "inertia");
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error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
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error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
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if (!cvcs.size() || (error_code != COLVARS_OK)) {
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cvm::error("Error: no valid components were provided "
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@ -732,7 +667,7 @@ int colvar::parse_analysis(std::string const &conf)
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} else {
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cvm::log("Unknown type of correlation function, \""+
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acf_type_str+"\".\n");
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cvm::set_error_bit(INPUT_ERROR);
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cvm::set_error_bits(INPUT_ERROR);
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}
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get_keyval(conf, "corrFuncOffset", acf_offset, 0);
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@ -803,9 +738,11 @@ int colvar::calc()
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// Note: if anything is added here, it should be added also in the SMP block of calc_colvars()
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int error_code = COLVARS_OK;
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if (is_enabled(f_cv_active)) {
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cvm::combine_errors(error_code, update_cvc_flags());
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cvm::combine_errors(error_code, calc_cvcs());
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cvm::combine_errors(error_code, collect_cvc_data());
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error_code |= update_cvc_flags();
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if (error_code != COLVARS_OK) return error_code;
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error_code |= calc_cvcs();
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if (error_code != COLVARS_OK) return error_code;
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error_code |= collect_cvc_data();
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}
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return error_code;
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}
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@ -818,15 +755,15 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
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cvm::log("Calculating colvar \""+this->name+"\", components "+
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cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");
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cvm::combine_errors(error_code, check_cvc_range(first_cvc, num_cvcs));
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error_code |= check_cvc_range(first_cvc, num_cvcs);
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if (error_code != COLVARS_OK) {
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return error_code;
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}
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cvm::combine_errors(error_code, calc_cvc_values(first_cvc, num_cvcs));
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cvm::combine_errors(error_code, calc_cvc_gradients(first_cvc, num_cvcs));
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cvm::combine_errors(error_code, calc_cvc_sys_forces(first_cvc, num_cvcs));
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cvm::combine_errors(error_code, calc_cvc_Jacobians(first_cvc, num_cvcs));
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error_code |= calc_cvc_values(first_cvc, num_cvcs);
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error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
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error_code |= calc_cvc_sys_forces(first_cvc, num_cvcs);
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error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
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if (cvm::debug())
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cvm::log("Done calculating colvar \""+this->name+"\".\n");
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@ -842,12 +779,11 @@ int colvar::collect_cvc_data()
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int error_code = COLVARS_OK;
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cvm::combine_errors(error_code, collect_cvc_values());
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cvm::combine_errors(error_code, collect_cvc_gradients());
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cvm::combine_errors(error_code, collect_cvc_sys_forces());
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cvm::combine_errors(error_code, collect_cvc_Jacobians());
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cvm::combine_errors(error_code, calc_colvar_properties());
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error_code |= collect_cvc_values();
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error_code |= collect_cvc_gradients();
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error_code |= collect_cvc_sys_forces();
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error_code |= collect_cvc_Jacobians();
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error_code |= calc_colvar_properties();
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if (cvm::debug())
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cvm::log("Done calculating colvar \""+this->name+"\"'s properties.\n");
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@ -1374,7 +1310,7 @@ bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) c
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if ( (!is_enabled(f_cv_lower_boundary)) || (!is_enabled(f_cv_upper_boundary)) ) {
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cvm::log("Error: checking periodicity for collective variable \""+this->name+"\" "
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"requires lower and upper boundaries to be defined.\n");
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cvm::set_error_bit(INPUT_ERROR);
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cvm::set_error_bits(INPUT_ERROR);
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}
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if (period > 0.0) {
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