Minor changes and fixes not relevant to LAMMPS (be2d155c) · Commits · 郑智淋 / lammps

lib/colvars/colvaratoms.cpp

+39 −6

Original line number	Diff line number	Diff line
		@@ -367,6 +367,7 @@ int cvm::atom_group::parse(std::string const &conf)
		cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR);
		}

		// 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);
		}
		}
		@@ -403,11 +404,21 @@ int cvm::atom_group::parse(std::string const &conf)
		}
		}

		// We need to know the fitting options to decide whether the group is scalable
		parse_error \|= parse_fitting_options(group_conf);

		if (is_available(f_ag_scalable_com) && !b_rotate) {
		enable(f_ag_scalable_com);
		enable(f_ag_scalable);
		}

		if (is_enabled(f_ag_scalable) && !b_dummy) {
		cvm::log("Enabling scalable calculation for group \""+this->key+"\".\n");
		index = (cvm::proxy)->init_atom_group(atoms_ids);
		}

		parse_error \|= parse_fitting_options(group_conf);
		bool b_print_atom_ids = false;
		get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent);

		// TODO move this to colvarparse object
		check_keywords(group_conf, key.c_str());
		@@ -427,6 +438,10 @@ int cvm::atom_group::parse(std::string const &conf)
		cvm::to_str(total_mass)+", total charge = "+
		cvm::to_str(total_charge)+".\n");

		if (b_print_atom_ids) {
		cvm::log("Internal definition of the atom group:\n");
		}

		cvm::decrease_depth();

		return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
		@@ -583,6 +598,21 @@ int cvm::atom_group::add_atom_name_residue_range(std::string const &psf_segid,
		}


		std::string const cvm::atom_group::print_atom_ids() const
		{
		size_t line_count = 0;
		std::ostringstream os("");
		for (size_t i = 0; i < atoms_ids.size(); i++) {
		os << " " << std::setw(9) << atoms_ids[i];
		if (++line_count == 7) {
		os << "\n";
		line_count = 0;
		}
		}
		return os.str();
		}


		int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
		{
		bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false);
		@@ -1118,8 +1148,7 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)
		log("Communicating a colvar force from atom group to the MD engine.\n");
		}

		if (b_dummy)
		return;
		if (b_dummy) return;

		if (noforce) {
		cvm::error("Error: sending a force to a group that has "
		@@ -1161,17 +1190,21 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)

		void cvm::atom_group::apply_force(cvm::rvector const &force)
		{
		if (b_dummy)
		return;
		if (cvm::debug()) {
		log("Communicating a colvar force from atom group to the MD engine.\n");
		}

		if (b_dummy) return;

		if (noforce) {
		cvm::error("Error: sending a force to a group that has "
		"\"disableForces\" defined.\n");
		"\"enableForces\" set to off.\n");
		return;
		}

		if (is_enabled(f_ag_scalable)) {
		(cvm::proxy)->apply_atom_group_force(index, force);
		return;
		}

		if (b_rotate) {

lib/colvars/colvaratoms.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -253,6 +253,8 @@ public:
		return atoms.size();
		}

		std::string const print_atom_ids() const;

		/// \brief If this option is on, this group merely acts as a wrapper
		/// for a fixed position; any calls to atoms within or to
		/// functions that return disaggregated data will fail

lib/colvars/colvarcomp.cpp

+3 −6

Original line number	Diff line number	Diff line
		@@ -84,15 +84,12 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
		if (is_available(f_cvc_scalable_com) && is_available(f_cvc_com_based)) {
		enable(f_cvc_scalable_com);
		enable(f_cvc_scalable);
		group->enable(f_ag_scalable_com);
		group->enable(f_ag_scalable);
		// The CVC makes the feature available;
		// the atom group will enable it unless it needs to compute a rotational fit
		group->provide(f_ag_scalable_com);
		}

		// TODO check for other types of parallelism here

		if (is_enabled(f_cvc_scalable)) {
		cvm::log("Will enable scalable calculation for group \""+group->key+"\".\n");
		}
		}

		if (group->parse(conf) == COLVARS_OK) {

lib/colvars/colvardeps.cpp

+4 −2

Original line number	Diff line number	Diff line
		@@ -449,8 +449,10 @@ void colvardeps::init_ag_requires() {

		// Features that are implemented (or not) by all atom groups
		feature_states[f_ag_active]->available = true;
		feature_states[f_ag_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
		feature_states[f_ag_scalable]->available = feature_states[f_ag_scalable_com]->available;
		// f_ag_scalable_com is provided by the CVC iff it is COM-based
		feature_states[f_ag_scalable_com]->available = false;
		// TODO make f_ag_scalable depend on f_ag_scalable_com (or something else)
		feature_states[f_ag_scalable]->available = true;
		}

lib/colvars/colvarmodule.cpp

+20 −11

Original line number	Diff line number	Diff line
		@@ -810,6 +810,7 @@ int colvarmodule::analyze()

		int colvarmodule::setup()
		{
		if (this->size() == 0) return cvm::get_error();
		// loop over all components of all colvars to reset masses of all groups
		for (std::vector<colvar *>::iterator cvi = colvars.begin();
		cvi != colvars.end(); cvi++) {
		@@ -867,25 +868,35 @@ int colvarmodule::reset()

		int colvarmodule::setup_input()
		{
		// name of input state file
		restart_in_name = proxy->input_prefix().size() ?
		std::string(proxy->input_prefix()+".colvars.state") :
		std::string("") ;
		if (this->size() == 0) return cvm::get_error();

		std::string restart_in_name("");

		// read the restart configuration, if available
		if (restart_in_name.size()) {
		if (proxy->input_prefix().size()) {
		// read the restart file
		restart_in_name = proxy->input_prefix();
		std::ifstream input_is(restart_in_name.c_str());
		if (!input_is.good()) {
		cvm::error("Error: in opening restart file \""+
		// try by adding the suffix
		input_is.clear();
		restart_in_name = restart_in_name+std::string(".colvars.state");
		input_is.open(restart_in_name.c_str());
		}

		if (!input_is.good()) {
		cvm::error("Error: in opening input file \""+
		std::string(restart_in_name)+"\".\n",
		FILE_ERROR);
		return COLVARS_ERROR;
		} else {
		cvm::log(cvm::line_marker);
		cvm::log("Restarting from file \""+restart_in_name+"\".\n");
		read_restart(input_is);
		if (cvm::get_error() != COLVARS_OK) {
		return COLVARS_ERROR;
		} else {
		proxy->input_prefix().clear();
		}
		cvm::log(cvm::line_marker);
		}
		@@ -897,7 +908,9 @@ int colvarmodule::setup_input()

		int colvarmodule::setup_output()
		{
		int error_code = 0;
		if (this->size() == 0) return cvm::get_error();

		int error_code = COLVARS_OK;

		// output state file (restart)
		restart_out_name = proxy->restart_output_prefix().size() ?
		@@ -1545,11 +1558,7 @@ std::list<std::string> colvarmodule::index_group_names;
		std::list<std::vector<int> > colvarmodule::index_groups;
		bool colvarmodule::use_scripted_forces = false;
		bool colvarmodule::scripting_after_biases = true;

		// file name prefixes
		std::string colvarmodule::output_prefix = "";
		std::string colvarmodule::restart_in_name = "";


		// i/o constants
		size_t const colvarmodule::it_width = 12;

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