Merge pull request #1190 from giacomofiorin/colvars-update (2635f7d1) · Commits · 郑智淋 / lammps

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

+31.9 KiB (607 KiB)

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lib/colvars/colvar.cpp

+93 −25

Original line number	Diff line number	Diff line
		@@ -427,7 +427,7 @@ int colvar::init_custom_function(std::string const &conf)
		if (x.size() != value_evaluators.size()) {
		cvm::error("Error: based on custom function type, expected "
		+ cvm::to_str(x.size()) + " scalar expressions, but "
		+ cvm::to_str(value_evaluators.size() + " were found.\n"));
		+ cvm::to_str(value_evaluators.size()) + " were found.\n");
		return INPUT_ERROR;
		}

		@@ -455,36 +455,42 @@ int colvar::init_grid_parameters(std::string const &conf)
		}

		lower_boundary.type(value());

		upper_boundary.type(value());
		upper_wall.type(value());

		if (is_enabled(f_cv_scalar)) {

		if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
		enable(f_cv_lower_boundary);
		}
		std::string lw_conf, uw_conf;

		if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0, parse_silent)) {
		cvm::log("Warning: lowerWallConstant and lowerWall are deprecated, "
		"please define a harmonicWalls bias instead.\n");
		if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
		enable(f_cv_upper_boundary);
		}

		std::string lw_conf, uw_conf;
		if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0,
		parse_silent)) {
		cvm::log("Reading legacy options lowerWall and lowerWallConstant: "
		"consider using a harmonicWalls restraint.\n");
		lower_wall.type(value());
		get_keyval(conf, "lowerWall", lower_wall, lower_boundary);
		if (!get_keyval(conf, "lowerWall", lower_wall, lower_boundary)) {
		cvm::log("Warning: lowerWall will need to be "
		"defined explicitly in the next release.\n");
		}
		lw_conf = std::string("\n\
		lowerWallConstant "+cvm::to_str(lower_wall_kwidthwidth)+"\n\
		lowerWalls "+cvm::to_str(lower_wall)+"\n");
		}

		if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
		enable(f_cv_upper_boundary);
		}

		if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0, parse_silent)) {
		cvm::log("Warning: upperWallConstant and upperWall are deprecated, "
		"please define a harmonicWalls bias instead.\n");
		if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0,
		parse_silent)) {
		cvm::log("Reading legacy options upperWall and upperWallConstant: "
		"consider using a harmonicWalls restraint.\n");
		upper_wall.type(value());
		get_keyval(conf, "upperWall", upper_wall, upper_boundary);
		if (!get_keyval(conf, "upperWall", upper_wall, upper_boundary)) {
		cvm::log("Warning: upperWall will need to be "
		"defined explicitly in the next release.\n");
		}
		uw_conf = std::string("\n\
		upperWallConstant "+cvm::to_str(upper_wall_kwidthwidth)+"\n\
		upperWalls "+cvm::to_str(upper_wall)+"\n");
		@@ -677,6 +683,7 @@ template<typename def_class_name> int colvar::init_components_type(std::string c
		if (cvcp != NULL) {
		cvcs.push_back(cvcp);
		cvcp->check_keywords(def_conf, def_config_key);
		cvcp->config_key = def_config_key;
		if (cvm::get_error()) {
		cvm::error("Error: in setting up component \""+
		std::string(def_config_key)+"\".\n", INPUT_ERROR);
		@@ -1022,13 +1029,13 @@ int colvar::calc()

		int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
		{
		colvarproxy *proxy = cvm::main()->proxy;

		int error_code = COLVARS_OK;
		if (cvm::debug())
		cvm::log("Calculating colvar \""+this->name+"\", components "+
		cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");

		colvarproxy *proxy = cvm::main()->proxy;
		int error_code = COLVARS_OK;

		error_code \|= check_cvc_range(first_cvc, num_cvcs);
		if (error_code != COLVARS_OK) {
		return error_code;
		@@ -1059,9 +1066,10 @@ int colvar::collect_cvc_data()
		if (cvm::debug())
		cvm::log("Calculating colvar \""+this->name+"\"'s properties.\n");

		colvarproxy *proxy = cvm::main()->proxy;
		int error_code = COLVARS_OK;

		if (cvm::step_relative() > 0) {
		if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
		// Total force depends on Jacobian derivative from previous timestep
		// collect_cvc_total_forces() uses the previous value of jd
		error_code \|= collect_cvc_total_forces();
		@@ -1069,6 +1077,10 @@ int colvar::collect_cvc_data()
		error_code \|= collect_cvc_values();
		error_code \|= collect_cvc_gradients();
		error_code \|= collect_cvc_Jacobians();
		if (proxy->total_forces_same_step()){
		// Use Jacobian derivative from this timestep
		error_code \|= collect_cvc_total_forces();
		}
		error_code \|= calc_colvar_properties();

		if (cvm::debug())
		@@ -1394,6 +1406,13 @@ int colvar::calc_colvar_properties()
		vr.reset(); // (already 0; added for clarity)
		}

		// Special case of a repeated timestep (eg. multiple NAMD "run" statements)
		// revert values of the extended coordinate and velocity prior to latest integration
		if (cvm::step_relative() == prev_timestep) {
		xr = prev_xr;
		vr = prev_vr;
		}

		// report the restraint center as "value"
		x_reported = xr;
		v_reported = vr;
		@@ -1450,7 +1469,6 @@ cvm::real colvar::update_forces_energy()
		// extended variable if there is one

		if (is_enabled(f_cv_extended_Lagrangian)) {

		if (cvm::debug()) {
		cvm::log("Updating extended-Lagrangian degree of freedom.\n");
		}
		@@ -1502,6 +1520,11 @@ cvm::real colvar::update_forces_energy()
		ft_reported = f_ext;
		}

		// backup in case we need to revert this integration timestep
		// if the same MD timestep is re-run
		prev_xr = xr;
		prev_vr = vr;

		// leapfrog: starting from x_i, f_i, v_(i-1/2)
		vr += (0.5 * dt) * f_ext / ext_mass;
		// Because of leapfrog, kinetic energy at time i is approximate
		@@ -1638,18 +1661,26 @@ int colvar::set_cvc_flags(std::vector<bool> const &flags)
		}


		void colvar::update_active_cvc_square_norm()
		{
		active_cvc_square_norm = 0.0;
		for (size_t i = 0; i < cvcs.size(); i++) {
		if (cvcs[i]->is_enabled()) {
		active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
		}
		}
		}


		int colvar::update_cvc_flags()
		{
		// Update the enabled/disabled status of cvcs if necessary
		if (cvc_flags.size()) {
		n_active_cvcs = 0;
		active_cvc_square_norm = 0.;

		for (size_t i = 0; i < cvcs.size(); i++) {
		cvcs[i]->set_enabled(f_cvc_active, cvc_flags[i]);
		if (cvcs[i]->is_enabled()) {
		n_active_cvcs++;
		active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
		}
		}
		if (!n_active_cvcs) {
		@@ -1657,12 +1688,49 @@ int colvar::update_cvc_flags()
		return COLVARS_ERROR;
		}
		cvc_flags.clear();

		update_active_cvc_square_norm();
		}

		return COLVARS_OK;
		}


		int colvar::update_cvc_config(std::vector<std::string> const &confs)
		{
		cvm::log("Updating configuration for colvar \""+name+"\"");

		if (confs.size() != cvcs.size()) {
		return cvm::error("Error: Wrong number of CVC config strings. "
		"For those CVCs that are not being changed, try passing "
		"an empty string.", INPUT_ERROR);
		}

		int error_code = COLVARS_OK;
		int num_changes = 0;
		for (size_t i = 0; i < cvcs.size(); i++) {
		if (confs[i].size()) {
		std::string conf(confs[i]);
		cvm::increase_depth();
		error_code \|= cvcs[i]->colvar::cvc::init(conf);
		error_code \|= cvcs[i]->check_keywords(conf,
		cvcs[i]->config_key.c_str());
		cvm::decrease_depth();
		num_changes++;
		}
		}

		if (num_changes == 0) {
		cvm::log("Warning: no changes were applied through modifycvcs; "
		"please check that its argument is a list of strings.\n");
		}

		update_active_cvc_square_norm();

		return error_code;
		}


		// ****************** METRIC FUNCTIONS ******************
		// Use the metrics defined by \link cvc \endlink objects

lib/colvars/colvar.h

+17 −3

Original line number	Diff line number	Diff line
		@@ -171,8 +171,12 @@ protected:
		// Options for extended_lagrangian
		/// Restraint center
		colvarvalue xr;
		/// Previous value of the restraint center;
		colvarvalue prev_xr;
		/// Velocity of the restraint center
		colvarvalue vr;
		/// Previous velocity of the restraint center
		colvarvalue prev_vr;
		/// Mass of the restraint center
		cvm::real ext_mass;
		/// Restraint force constant
		@@ -352,6 +356,9 @@ public:
		/// \brief Updates the flags in the CVC objects, and their number
		int update_cvc_flags();

		/// \brief Modify the configuration of CVCs (currently, only base class data)
		int update_cvc_config(std::vector<std::string> const &confs);

		protected:
		/// \brief Number of CVC objects with an active flag
		size_t n_active_cvcs;
		@@ -359,10 +366,17 @@ protected:
		/// Sum of square coefficients for active cvcs
		cvm::real active_cvc_square_norm;

		/// Update the sum of square coefficients for active cvcs
		void update_active_cvc_square_norm();

		/// \brief Absolute timestep number when this colvar was last updated
		int prev_timestep;

		public:

		/// \brief Return the number of CVC objects defined
		inline size_t num_cvcs() const { return cvcs.size(); }

		/// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags)
		inline size_t num_active_cvcs() const { return n_active_cvcs; }

lib/colvars/colvaratoms.cpp

+3 −1

Original line number	Diff line number	Diff line
		@@ -21,6 +21,8 @@ cvm::atom::atom()
		{
		index = -1;
		id = -1;
		mass = 1.0;
		charge = 1.0;
		reset_data();
		}

		@@ -395,7 +397,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
		}

		// NOTE: calls to add_atom() and/or add_atom_id() are in the proxy-implemented function
		cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
		parse_error \|= cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
		}
		}

lib/colvars/colvaratoms.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -90,7 +90,7 @@ public:
		/// Destructor
		~atom();

		/// Set mutable data (everything except id and mass) to zero; update mass
		/// Set mutable data (everything except id and mass) to zero
		inline void reset_data()
		{
		pos = cvm::atom_pos(0.0);

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