update colvars to version 2016-08-10 (ec2a6b9f) · Commits · 郑智淋 / lammps

doc/src/PDF/colvars-refman-lammps.pdf

+251 B (521 KiB)

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lib/colvars/colvar.cpp

+57 −121

Original line number	Diff line number	Diff line
		@@ -43,7 +43,8 @@ colvar::colvar(std::string const &conf)
		kinetic_energy = 0.0;
		potential_energy = 0.0;

		cvm::combine_errors(error_code, init_components(conf));
		error_code \|= init_components(conf);
		if (error_code != COLVARS_OK) return;

		size_t i;

		@@ -492,110 +493,44 @@ int colvar::init_components(std::string const &conf)
		{
		int error_code = COLVARS_OK;

		cvm::combine_errors(error_code,
		init_components_type<distance>(conf,
		"distance", "distance"));
		cvm::combine_errors(error_code,
		init_components_type<distance_vec>(conf,
		"distance vector", "distanceVec"));
		cvm::combine_errors(error_code,
		init_components_type<cartesian>(conf,
		"Cartesian coordinates", "cartesian"));
		cvm::combine_errors(error_code,
		init_components_type<distance_dir>(conf,
		"distance vector "
		"direction", "distanceDir"));
		cvm::combine_errors(error_code,
		init_components_type<distance_z>(conf,
		"distance projection "
		"on an axis", "distanceZ"));
		cvm::combine_errors(error_code,
		init_components_type<distance_xy>(conf,
		"distance projection "
		"on a plane", "distanceXY"));
		cvm::combine_errors(error_code,
		init_components_type<distance_inv>(conf,
		"average distance "
		"weighted by inverse power",
		"distanceInv"));
		cvm::combine_errors(error_code,
		init_components_type<distance_pairs>(conf,
		"N1xN2-long vector "
		"of pairwise distances",
		"distancePairs"));

		cvm::combine_errors(error_code,
		init_components_type<coordnum>(conf,
		"coordination "
		"number", "coordNum"));
		cvm::combine_errors(error_code,
		init_components_type<selfcoordnum>(conf,
		"self-coordination "
		"number", "selfCoordNum"));

		cvm::combine_errors(error_code,
		init_components_type<angle>(conf,
		"angle", "angle"));
		cvm::combine_errors(error_code,
		init_components_type<dipole_angle>(conf,
		"dipole angle", "dipoleAngle"));
		cvm::combine_errors(error_code,
		init_components_type<dihedral>(conf,
		"dihedral", "dihedral"));

		cvm::combine_errors(error_code,
		init_components_type<h_bond>(conf,
		"hydrogen bond", "hBond"));

		// cvm::combine_errors(error_code, init_components_type<alpha_dihedrals>(conf, "alpha helix", "alphaDihedrals"));
		cvm::combine_errors(error_code,
		init_components_type<alpha_angles>(conf,
		"alpha helix", "alpha"));

		cvm::combine_errors(error_code,
		init_components_type<dihedPC>(conf,
		"dihedral "
		"principal component", "dihedralPC"));

		cvm::combine_errors(error_code,
		init_components_type<orientation>(conf,
		"orientation", "orientation"));
		cvm::combine_errors(error_code,
		init_components_type<orientation_angle>(conf,
		"orientation "
		"angle", "orientationAngle"));
		cvm::combine_errors(error_code,
		init_components_type<orientation_proj>(conf,
		"orientation "
		"projection", "orientationProj"));
		cvm::combine_errors(error_code,
		init_components_type<tilt>(conf,
		"tilt", "tilt"));
		cvm::combine_errors(error_code,
		init_components_type<spin_angle>(conf,
		"spin angle", "spinAngle"));

		cvm::combine_errors(error_code,
		init_components_type<rmsd>(conf,
		"RMSD", "rmsd"));

		// cvm::combine_errors(error_code, init_components_type <logmsd>(conf,"logarithm of MSD", "logmsd"));

		cvm::combine_errors(error_code,
		init_components_type<gyration>(conf,
		"radius of "
		"gyration", "gyration"));
		cvm::combine_errors(error_code,
		init_components_type<inertia>(conf,
		"moment of "
		"inertia", "inertia"));
		cvm::combine_errors(error_code,
		init_components_type<inertia_z>(conf,
		"moment of inertia around an axis",
		"inertiaZ"));
		cvm::combine_errors(error_code,
		init_components_type<eigenvector>(conf,
		"eigenvector", "eigenvector"));
		error_code \|= init_components_type<distance>(conf, "distance", "distance");
		error_code \|= init_components_type<distance_vec>(conf, "distance vector", "distanceVec");
		error_code \|= init_components_type<cartesian>(conf, "Cartesian coordinates", "cartesian");
		error_code \|= init_components_type<distance_dir>(conf, "distance vector "
		"direction", "distanceDir");
		error_code \|= init_components_type<distance_z>(conf, "distance projection "
		"on an axis", "distanceZ");
		error_code \|= init_components_type<distance_xy>(conf, "distance projection "
		"on a plane", "distanceXY");
		error_code \|= init_components_type<distance_inv>(conf, "average distance "
		"weighted by inverse power", "distanceInv");
		error_code \|= init_components_type<distance_pairs>(conf, "N1xN2-long vector "
		"of pairwise distances", "distancePairs");
		error_code \|= init_components_type<coordnum>(conf, "coordination "
		"number", "coordNum");
		error_code \|= init_components_type<selfcoordnum>(conf, "self-coordination "
		"number", "selfCoordNum");
		error_code \|= init_components_type<angle>(conf, "angle", "angle");
		error_code \|= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
		error_code \|= init_components_type<dihedral>(conf, "dihedral", "dihedral");
		error_code \|= init_components_type<h_bond>(conf, "hydrogen bond", "hBond");
		error_code \|= init_components_type<alpha_angles>(conf, "alpha helix", "alpha");
		error_code \|= init_components_type<dihedPC>(conf, "dihedral "
		"principal component", "dihedralPC");
		error_code \|= init_components_type<orientation>(conf, "orientation", "orientation");
		error_code \|= init_components_type<orientation_angle>(conf, "orientation "
		"angle", "orientationAngle");
		error_code \|= init_components_type<orientation_proj>(conf, "orientation "
		"projection", "orientationProj");
		error_code \|= init_components_type<tilt>(conf, "tilt", "tilt");
		error_code \|= init_components_type<spin_angle>(conf, "spin angle", "spinAngle");
		error_code \|= init_components_type<rmsd>(conf, "RMSD", "rmsd");
		error_code \|= init_components_type<gyration>(conf, "radius of "
		"gyration", "gyration");
		error_code \|= init_components_type<inertia>(conf, "moment of "
		"inertia", "inertia");
		error_code \|= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
		error_code \|= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");

		if (!cvcs.size() \|\| (error_code != COLVARS_OK)) {
		cvm::error("Error: no valid components were provided "
		@@ -732,7 +667,7 @@ int colvar::parse_analysis(std::string const &conf)
		} else {
		cvm::log("Unknown type of correlation function, \""+
		acf_type_str+"\".\n");
		cvm::set_error_bit(INPUT_ERROR);
		cvm::set_error_bits(INPUT_ERROR);
		}

		get_keyval(conf, "corrFuncOffset", acf_offset, 0);
		@@ -803,9 +738,11 @@ int colvar::calc()
		// Note: if anything is added here, it should be added also in the SMP block of calc_colvars()
		int error_code = COLVARS_OK;
		if (is_enabled(f_cv_active)) {
		cvm::combine_errors(error_code, update_cvc_flags());
		cvm::combine_errors(error_code, calc_cvcs());
		cvm::combine_errors(error_code, collect_cvc_data());
		error_code \|= update_cvc_flags();
		if (error_code != COLVARS_OK) return error_code;
		error_code \|= calc_cvcs();
		if (error_code != COLVARS_OK) return error_code;
		error_code \|= collect_cvc_data();
		}
		return error_code;
		}
		@@ -818,15 +755,15 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
		cvm::log("Calculating colvar \""+this->name+"\", components "+
		cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");

		cvm::combine_errors(error_code, check_cvc_range(first_cvc, num_cvcs));
		error_code \|= check_cvc_range(first_cvc, num_cvcs);
		if (error_code != COLVARS_OK) {
		return error_code;
		}

		cvm::combine_errors(error_code, calc_cvc_values(first_cvc, num_cvcs));
		cvm::combine_errors(error_code, calc_cvc_gradients(first_cvc, num_cvcs));
		cvm::combine_errors(error_code, calc_cvc_sys_forces(first_cvc, num_cvcs));
		cvm::combine_errors(error_code, calc_cvc_Jacobians(first_cvc, num_cvcs));
		error_code \|= calc_cvc_values(first_cvc, num_cvcs);
		error_code \|= calc_cvc_gradients(first_cvc, num_cvcs);
		error_code \|= calc_cvc_sys_forces(first_cvc, num_cvcs);
		error_code \|= calc_cvc_Jacobians(first_cvc, num_cvcs);

		if (cvm::debug())
		cvm::log("Done calculating colvar \""+this->name+"\".\n");
		@@ -842,12 +779,11 @@ int colvar::collect_cvc_data()

		int error_code = COLVARS_OK;

		cvm::combine_errors(error_code, collect_cvc_values());
		cvm::combine_errors(error_code, collect_cvc_gradients());
		cvm::combine_errors(error_code, collect_cvc_sys_forces());
		cvm::combine_errors(error_code, collect_cvc_Jacobians());

		cvm::combine_errors(error_code, calc_colvar_properties());
		error_code \|= collect_cvc_values();
		error_code \|= collect_cvc_gradients();
		error_code \|= collect_cvc_sys_forces();
		error_code \|= collect_cvc_Jacobians();
		error_code \|= calc_colvar_properties();

		if (cvm::debug())
		cvm::log("Done calculating colvar \""+this->name+"\"'s properties.\n");
		@@ -1374,7 +1310,7 @@ bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) c
		if ( (!is_enabled(f_cv_lower_boundary)) \|\| (!is_enabled(f_cv_upper_boundary)) ) {
		cvm::log("Error: checking periodicity for collective variable \""+this->name+"\" "
		"requires lower and upper boundaries to be defined.\n");
		cvm::set_error_bit(INPUT_ERROR);
		cvm::set_error_bits(INPUT_ERROR);
		}

		if (period > 0.0) {

lib/colvars/colvaratoms.cpp

+6 −6

Original line number	Diff line number	Diff line
		@@ -297,7 +297,7 @@ int cvm::atom_group::parse(std::string const &conf)
		std::string numbers_conf = "";
		size_t pos = 0;
		while (key_lookup(group_conf, "atomNumbers", numbers_conf, pos)) {
		cvm::combine_errors(parse_error, add_atom_numbers(numbers_conf));
		parse_error \|= add_atom_numbers(numbers_conf);
		numbers_conf = "";
		}
		}
		@@ -306,7 +306,7 @@ int cvm::atom_group::parse(std::string const &conf)
		std::string index_group_name;
		if (get_keyval(group_conf, "indexGroup", index_group_name)) {
		// use an index group from the index file read globally
		cvm::combine_errors(parse_error, add_index_group(index_group_name));
		parse_error \|= add_index_group(index_group_name);
		}
		}

		@@ -315,7 +315,7 @@ int cvm::atom_group::parse(std::string const &conf)
		size_t pos = 0;
		while (key_lookup(group_conf, "atomNumbersRange",
		range_conf, pos)) {
		cvm::combine_errors(parse_error, add_atom_numbers_range(range_conf));
		parse_error \|= add_atom_numbers_range(range_conf);
		range_conf = "";
		}
		}
		@@ -342,8 +342,8 @@ int cvm::atom_group::parse(std::string const &conf)
		cvm::error("Error: more instances of \"atomNameResidueRange\" than "
		"values of \"psfSegID\".\n", INPUT_ERROR);
		} else {
		cvm::combine_errors(parse_error, add_atom_name_residue_range(psf_segids.size() ?
		*psii : std::string(""), range_conf));
		parse_error \|= add_atom_name_residue_range(psf_segids.size() ?
		*psii : std::string(""), range_conf);
		if (psf_segids.size()) psii++;
		}
		range_conf = "";
		@@ -407,7 +407,7 @@ int cvm::atom_group::parse(std::string const &conf)
		index = (cvm::proxy)->init_atom_group(atoms_ids);
		}

		cvm::combine_errors(parse_error, parse_fitting_options(group_conf));
		parse_error \|= parse_fitting_options(group_conf);

		// TODO move this to colvarparse object
		check_keywords(group_conf, key.c_str());

lib/colvars/colvarbias.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -203,7 +203,7 @@ cvm::real colvarbias::energy_difference(std::string const &conf)
		}


		// So far, these are only implemented in colvarsbias_abf
		// So far, these are only implemented in colvarbias_abf
		int colvarbias::bin_num()
		{
		cvm::error("Error: bin_num() not implemented.\n");

lib/colvars/colvarbias_histogram.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -104,7 +104,7 @@ int colvarbias_histogram::update()
		{
		int error_code = COLVARS_OK;
		// update base class
		cvm::combine_errors(error_code, colvarbias::update());
		error_code \|= colvarbias::update();

		if (cvm::debug()) {
		cvm::log("Updating histogram bias " + this->name);
		@@ -157,7 +157,7 @@ int colvarbias_histogram::update()
		write_output_files();
		}

		cvm::combine_errors(error_code, cvm::get_error());
		error_code \|= cvm::get_error();
		return error_code;
		}

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