Merge pull request #1909 from giacomofiorin/colvars-update (fb3a8f5b) · Commits · 郑智淋 / lammps

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

+11.5 KiB (673 KiB)

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lib/colvars/Makefile.deps

+23 −11

Original line number	Diff line number	Diff line
		@@ -27,46 +27,58 @@ $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
		$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
		colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
		colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
		colvarproxy.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp
		colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
		colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
		colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
		colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
		colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h colvardeps.h \
		colvar.h colvarcomp.h colvar_arithmeticpath.h
		colvar.h colvarcomp.h colvar_arithmeticpath.h colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
		colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
		colvar_arithmeticpath.h
		colvar_arithmeticpath.h colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
		colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
		colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
		colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
		colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
		colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
		colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
		colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
		colvar_arithmeticpath.h colvarscript.h colvarbias.h
		colvar_arithmeticpath.h colvar_geometricpath.h colvarscript.h \
		colvarbias.h
		$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
		colvarparse.h colvarparams.h
		$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
		colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
		colvarproxy.h colvar_arithmeticpath.h colvargrid.h
		colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h \
		colvargrid.h
		$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
		colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
		colvarparams.h colvarproxy.h colvar.h colvardeps.h colvarbias.h \
		colvarbias_abf.h colvargrid.h colvar_UIestimator.h colvarbias_alb.h \
		colvarbias_histogram.h colvarbias_meta.h colvarbias_restraint.h \
		colvarscript.h colvaratoms.h colvarcomp.h colvar_arithmeticpath.h
		colvarscript.h colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \
		colvar_geometricpath.h
		$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
		$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \

lib/colvars/colvar.cpp

+55 −43

Original line number	Diff line number	Diff line
		@@ -33,6 +33,8 @@ colvar::colvar()
		dev_null = 0.0;
		#endif

		expand_boundaries = false;

		description = "uninitialized colvar";
		init_dependencies();
		}
		@@ -474,6 +476,8 @@ int colvar::init_custom_function(std::string const &conf)

		int colvar::init_grid_parameters(std::string const &conf)
		{
		int error_code = COLVARS_OK;

		colvarmodule *cv = cvm::main();

		cvm::real default_width = width;
		@@ -527,15 +531,18 @@ int colvar::init_grid_parameters(std::string const &conf)
		disable(f_cv_hard_upper_boundary);
		}

		// Parse legacy wall options and set up a harmonicWalls bias if needed
		cvm::real lower_wall_k = 0.0, upper_wall_k = 0.0;
		cvm::real lower_wall = 0.0, upper_wall = 0.0;
		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(caution: force constant would then be scaled by width^2).\n");
		lower_wall.type(value());
		if (!get_keyval(conf, "lowerWall", lower_wall, lower_boundary)) {
		cvm::log("Warning: lowerWall will need to be "
		"defined explicitly in the next release.\n");
		"consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
		if (!get_keyval(conf, "lowerWall", lower_wall)) {
		error_code != cvm::error("Error: the value of lowerWall must be set "
		"explicitly.\n", INPUT_ERROR);
		}
		lw_conf = std::string("\n\
		lowerWallConstant "+cvm::to_str(lower_wall_kwidthwidth)+"\n\
		@@ -545,11 +552,10 @@ int colvar::init_grid_parameters(std::string const &conf)
		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(caution: force constant would then be scaled by width^2).\n");
		upper_wall.type(value());
		if (!get_keyval(conf, "upperWall", upper_wall, upper_boundary)) {
		cvm::log("Warning: upperWall will need to be "
		"defined explicitly in the next release.\n");
		"consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
		if (!get_keyval(conf, "upperWall", upper_wall)) {
		error_code != cvm::error("Error: the value of upperWall must be set "
		"explicitly.\n", INPUT_ERROR);
		}
		uw_conf = std::string("\n\
		upperWallConstant "+cvm::to_str(upper_wall_kwidthwidth)+"\n\
		@@ -558,12 +564,11 @@ int colvar::init_grid_parameters(std::string const &conf)

		if (lw_conf.size() && uw_conf.size()) {
		if (lower_wall >= upper_wall) {
		cvm::error("Error: the upper wall, "+
		error_code \|= cvm::error("Error: the upper wall, "+
		cvm::to_str(upper_wall)+
		", is not higher than the lower wall, "+
		cvm::to_str(lower_wall)+".\n",
		INPUT_ERROR);
		return INPUT_ERROR;
		}
		}

		@@ -575,7 +580,7 @@ harmonicWalls {\n\
		colvars "+this->name+"\n"+lw_conf+uw_conf+"\
		timeStepFactor "+cvm::to_str(time_step_factor)+"\n"+
		"}\n");
		cv->append_new_config(walls_conf);
		error_code \|= cv->append_new_config(walls_conf);
		}
		}

		@@ -588,29 +593,27 @@ harmonicWalls {\n\
		// consistency checks for boundaries and walls
		if (is_enabled(f_cv_lower_boundary) && is_enabled(f_cv_upper_boundary)) {
		if (lower_boundary >= upper_boundary) {
		cvm::error("Error: the upper boundary, "+
		error_code \|= cvm::error("Error: the upper boundary, "+
		cvm::to_str(upper_boundary)+
		", is not higher than the lower boundary, "+
		cvm::to_str(lower_boundary)+".\n",
		INPUT_ERROR);
		return INPUT_ERROR;
		}
		}

		get_keyval(conf, "expandBoundaries", expand_boundaries, false);
		get_keyval(conf, "expandBoundaries", expand_boundaries, expand_boundaries);
		if (expand_boundaries && periodic_boundaries()) {
		cvm::error("Error: trying to expand boundaries that already "
		error_code \|= cvm::error("Error: trying to expand boundaries that already "
		"cover a whole period of a periodic colvar.\n",
		INPUT_ERROR);
		return INPUT_ERROR;
		}

		if (expand_boundaries && is_enabled(f_cv_hard_lower_boundary) &&
		is_enabled(f_cv_hard_upper_boundary)) {
		cvm::error("Error: inconsistent configuration "
		"(trying to expand boundaries with both "
		"hardLowerBoundary and hardUpperBoundary enabled).\n",
		INPUT_ERROR);
		return INPUT_ERROR;
		error_code \|= cvm::error("Error: inconsistent configuration "
		"(trying to expand boundaries, but both "
		"hardLowerBoundary and hardUpperBoundary "
		"are enabled).\n", INPUT_ERROR);
		}

		return COLVARS_OK;
		@@ -2077,12 +2080,12 @@ void colvar::wrap(colvarvalue &x_unwrapped) const

		// ****************** INPUT FUNCTIONS ******************

		std::istream & colvar::read_restart(std::istream &is)
		std::istream & colvar::read_state(std::istream &is)
		{
		size_t const start_pos = is.tellg();

		std::string conf;
		if ( !(is >> colvarparse::read_block("colvar", conf)) ) {
		if ( !(is >> colvarparse::read_block("colvar", &conf)) ) {
		// this is not a colvar block
		is.clear();
		is.seekg(start_pos, std::ios::beg);
		@@ -2092,15 +2095,24 @@ std::istream & colvar::read_restart(std::istream &is)

		{
		std::string check_name = "";
		if ( (get_keyval(conf, "name", check_name,
		std::string(""), colvarparse::parse_silent)) &&
		(check_name != name) ) {
		cvm::error("Error: the state file does not match the "
		"configuration file, at colvar \""+name+"\".\n");
		}
		get_keyval(conf, "name", check_name,
		std::string(""), colvarparse::parse_silent);
		if (check_name.size() == 0) {
		cvm::error("Error: Collective variable in the "
		"restart file without any identifier.\n");
		"restart file without any identifier.\n", INPUT_ERROR);
		is.clear();
		is.seekg(start_pos, std::ios::beg);
		is.setstate(std::ios::failbit);
		return is;
		}

		if (check_name != name) {
		if (cvm::debug()) {
		cvm::log("Ignoring state of colvar \""+check_name+
		"\": this colvar is named \""+name+"\".\n");
		}
		is.seekg(start_pos, std::ios::beg);
		return is;
		}
		}

		@@ -2199,7 +2211,7 @@ std::istream & colvar::read_traj(std::istream &is)

		// ****************** OUTPUT FUNCTIONS ******************

		std::ostream & colvar::write_restart(std::ostream &os) {
		std::ostream & colvar::write_state(std::ostream &os) {

		os << "colvar {\n"
		<< " name " << name << "\n"

lib/colvars/colvar.h

+2 −10

Original line number	Diff line number	Diff line
		@@ -229,17 +229,9 @@ public:

		/// \brief Location of the lower boundary
		colvarvalue lower_boundary;
		/// \brief Location of the lower wall
		colvarvalue lower_wall;
		/// \brief Force constant for the lower boundary potential (\|x-xb\|^2)
		cvm::real lower_wall_k;

		/// \brief Location of the upper boundary
		colvarvalue upper_boundary;
		/// \brief Location of the upper wall
		colvarvalue upper_wall;
		/// \brief Force constant for the upper boundary potential (\|x-xb\|^2)
		cvm::real upper_wall_k;

		/// \brief Is the interval defined by the two boundaries periodic?
		bool periodic_boundaries() const;
		@@ -453,9 +445,9 @@ public:
		std::ostream & write_traj_label(std::ostream &os);

		/// Read the collective variable from a restart file
		std::istream & read_restart(std::istream &is);
		std::istream & read_state(std::istream &is);
		/// Write the collective variable to a restart file
		std::ostream & write_restart(std::ostream &os);
		std::ostream & write_state(std::ostream &os);

		/// Write output files (if defined, e.g. in analysis mode)
		int write_output_files();

lib/colvars/colvarbias.cpp

+66 −19

Original line number	Diff line number	Diff line
		@@ -15,8 +15,10 @@


		colvarbias::colvarbias(char const *key)
		: bias_type(to_lower_cppstr(key))
		{
		bias_type = to_lower_cppstr(key);
		state_keyword = bias_type;

		description = "uninitialized " + cvm::to_str(key) + " bias";
		init_dependencies();
		rank = 1;
		@@ -25,6 +27,7 @@ colvarbias::colvarbias(char const *key)
		b_output_energy = false;
		reset();
		state_file_step = 0L;
		matching_state = false;
		}


		@@ -80,10 +83,21 @@ int colvarbias::init(std::string const &conf)
		cvm::log("Reinitializing bias \""+name+"\".\n");
		}

		colvar_values.resize(num_variables());

		for (i = 0; i < num_variables(); i++) {
		colvar_values[i].type(colvars[i]->value().type());
		colvar_forces[i].type(colvar_values[i].type());
		previous_colvar_forces[i].type(colvar_values[i].type());
		}

		output_prefix = cvm::output_prefix();

		get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);

		// Disabled by default in base class; default value can be overridden by derived class constructor
		get_keyval_feature(this, conf, "bypassExtendedLagrangian", f_cvb_bypass_ext_lagrangian, is_enabled(f_cvb_bypass_ext_lagrangian), parse_silent);

		get_keyval(conf, "timeStepFactor", time_step_factor, 1);
		if (time_step_factor < 1) {
		cvm::error("Error: timeStepFactor must be 1 or greater.\n");
		@@ -114,6 +128,11 @@ int colvarbias::init_dependencies() {
		init_feature(f_cvb_apply_force, "apply force", f_type_user);
		require_feature_children(f_cvb_apply_force, f_cv_gradient);

		init_feature(f_cvb_bypass_ext_lagrangian, "bypass extended-Lagrangian coordinates", f_type_user);
		// The exclusion below prevents the inconsistency where biasing forces are applied onto
		// the actual colvar, while total forces are measured on the extended coordinate
		exclude_feature_self(f_cvb_bypass_ext_lagrangian, f_cvb_get_total_force);

		init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic);
		require_feature_children(f_cvb_get_total_force, f_cv_total_force);

		@@ -158,6 +177,12 @@ int colvarbias::init_dependencies() {
		// only compute TI samples when deriving from colvarbias_ti
		feature_states[f_cvb_calc_ti_samples].available = false;

		// The feature f_cvb_bypass_ext_lagrangian is only implemented by some derived classes
		// (initially, harmonicWalls)
		feature_states[f_cvb_bypass_ext_lagrangian].available = false;
		// disabled by default; can be changed by derived classes that implement it
		feature_states[f_cvb_bypass_ext_lagrangian].enabled = false;

		return COLVARS_OK;
		}

		@@ -265,6 +290,11 @@ int colvarbias::update()

		has_data = true;

		// Update the cached colvar values
		for (size_t i = 0; i < num_variables(); i++) {
		colvar_values[i] = colvars[i]->value();
		}

		error_code \|= calc_energy(NULL);
		error_code \|= calc_forces(NULL);

		@@ -304,9 +334,11 @@ void colvarbias::communicate_forces()
		// may send forces to the same colvar
		// which is why rescaling has to happen now: the colvar is not
		// aware of this bias' time_step_factor
		if (is_enabled(f_cvb_bypass_ext_lagrangian)) {
		variables(i)->add_bias_force_actual_value(cvm::real(time_step_factor) * colvar_forces[i]);
		} else {
		variables(i)->add_bias_force(cvm::real(time_step_factor) * colvar_forces[i]);
		}
		for (i = 0; i < num_variables(); i++) {
		previous_colvar_forces[i] = colvar_forces[i];
		}
		}
		@@ -368,20 +400,27 @@ std::string const colvarbias::get_state_params() const

		int colvarbias::set_state_params(std::string const &conf)
		{
		std::string new_name = "";
		if (colvarparse::get_keyval(conf, "name", new_name,
		std::string(""), colvarparse::parse_silent) &&
		(new_name != this->name)) {
		cvm::error("Error: in the state file, the "
		"\""+bias_type+"\" block has a different name, \""+new_name+
		"\": different system?\n", INPUT_ERROR);
		}
		matching_state = false;

		if (name.size() == 0) {
		std::string check_name = "";
		colvarparse::get_keyval(conf, "name", check_name,
		std::string(""), colvarparse::parse_silent);

		if (check_name.size() == 0) {
		cvm::error("Error: \""+bias_type+"\" block within the restart file "
		"has no identifiers.\n", INPUT_ERROR);
		}

		if (check_name != this->name) {
		if (cvm::debug()) {
		cvm::log("Ignoring state of bias \""+check_name+
		"\": this bias is named \""+name+"\".\n");
		}
		return COLVARS_OK;
		}

		matching_state = true;

		colvarparse::get_keyval(conf, "step", state_file_step,
		cvm::step_absolute(), colvarparse::parse_silent);

		@@ -396,7 +435,7 @@ std::ostream & colvarbias::write_state(std::ostream &os)
		}
		os.setf(std::ios::scientific, std::ios::floatfield);
		os.precision(cvm::cv_prec);
		os << bias_type << " {\n"
		os << state_keyword << " {\n"
		<< " configuration {\n";
		std::istringstream is(get_state_params());
		std::string line;
		@@ -415,13 +454,12 @@ std::istream & colvarbias::read_state(std::istream &is)
		size_t const start_pos = is.tellg();

		std::string key, brace, conf;
		if ( !(is >> key) \|\| !(key == bias_type) \|\|
		if ( !(is >> key) \|\| !(key == state_keyword \|\| key == bias_type) \|\|
		!(is >> brace) \|\| !(brace == "{") \|\|
		!(is >> colvarparse::read_block("configuration", conf)) \|\|
		!(is >> colvarparse::read_block("configuration", &conf)) \|\|
		(set_state_params(conf) != COLVARS_OK) ) {
		if (key != bias_type)
		cvm::log("Found key \"" + key + "\" instead of \"" + bias_type + "\"\n");
		cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
		cvm::error("Error: in reading state configuration for \""+bias_type+
		"\" bias \""+
		this->name+"\" at position "+
		cvm::to_str(static_cast<size_t>(is.tellg()))+
		" in stream.\n", INPUT_ERROR);
		@@ -431,6 +469,15 @@ std::istream & colvarbias::read_state(std::istream &is)
		return is;
		}

		if (matching_state == false) {
		// This state is not for this bias
		is.seekg(start_pos, std::ios::beg);
		return is;
		}

		cvm::log("Restarting "+bias_type+" bias \""+name+"\" from step number "+
		cvm::to_str(state_file_step)+".\n");

		if (!read_state_data(is)) {
		cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+
		this->name+"\" at position "+

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