(974e1eb0) · Commits · 郑智淋 / lammps

lib/colvars/colvarmodule.cpp

+14 −7

Original line number	Diff line number	Diff line
		@@ -598,7 +598,7 @@ int colvarmodule::calc() {
		write_traj(cv_traj_os);
		}

		if (restart_out_freq) {
		if (restart_out_freq && cv_traj_os.is_open()) {
		// flush the trajectory file if we are at the restart frequency
		if ( (cvm::step_relative() > 0) &&
		((cvm::step_absolute() % restart_out_freq) == 0) ) {
		@@ -683,8 +683,10 @@ int colvarmodule::reset()
		index_groups.clear();
		index_group_names.clear();

		if (cv_traj_os.is_open()) {
		// Do not close file here, as we might not be done with it yet.
		cv_traj_os.flush();
		}

		return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
		}
		@@ -826,8 +828,11 @@ int colvarmodule::write_output_files()
		}
		cvm::decrease_depth();

		if (cv_traj_os.is_open()) {
		// do not close to avoid problems with multiple NAMD runs
		cv_traj_os.flush();
		}

		return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
		}

		@@ -985,8 +990,9 @@ std::ostream & colvarmodule::write_traj_label(std::ostream &os)
		(*bi)->write_traj_label(os);
		}
		os << "\n";
		if (cvm::debug())
		if (cvm::debug()) {
		os.flush();
		}
		cvm::decrease_depth();
		return os;
		}
		@@ -1010,8 +1016,9 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
		(*bi)->write_traj(os);
		}
		os << "\n";
		if (cvm::debug())
		if (cvm::debug()) {
		os.flush();
		}
		cvm::decrease_depth();
		return os;
		}

lib/colvars/colvarmodule.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@
		#define COLVARMODULE_H

		#ifndef COLVARS_VERSION
		#define COLVARS_VERSION "2015-02-27"
		#define COLVARS_VERSION "2015-03-15"
		#endif

		#ifndef COLVARS_DEBUG

lib/colvars/colvarscript.cpp

+70 −57

Original line number	Diff line number	Diff line
		@@ -25,45 +25,7 @@ int colvarscript::run(int argc, char const *argv[]) {
		}

		if (argc < 2) {
		result = "usage: "+std::string(argv[0])+" <subcommand> [args...]\n\
		\n\
		Managing the colvars module:\n\
		configfile <file name> -- read configuration from a file\n\
		config <string> -- read configuration from the given string\n\
		reset -- delete all internal configuration\n\
		delete -- delete this colvars module instance\n\
		version -- return version of colvars code\n\
		\n\
		Input and output:\n\
		list -- return a list of all variables\n\
		list biases -- return a list of all biases\n\
		load <file name> -- load a state file (requires configuration)\n\
		update -- recalculate colvars and biases based\n\
		printframe -- return a summary of the current frame\n\
		printframelabels -- return labels to annotate printframe's output\n";

		if (proxy->frame() != COLVARS_NOT_IMPLEMENTED) {
		result += "\
		frame -- return current frame number\n\
		frame <new_frame> -- set frame number\n";
		}

		result += "\n\
		Accessing collective variables:\n\
		colvar <name> value -- return the current value of colvar <name>\n\
		colvar <name> update -- recalculate colvar <name>\n\
		colvar <name> type -- return the type of colvar <name>\n\
		colvar <name> delete -- delete colvar <name>\n\
		colvar <name> addforce <F> -- apply given force on colvar <name>\n\
		colvar <name> getconfig -- return config string of colvar <name>\n\
		\n\
		Accessing biases:\n\
		bias <name> energy -- return the current energy of bias <name>\n\
		bias <name> update -- recalculate bias <name>\n\
		bias <name> delete -- delete bias <name>\n\
		bias <name> getconfig -- return config string of bias <name>\n\
		\n\
		";
		result = help_string();
		return COLVARSCRIPT_OK;
		}

		@@ -117,7 +79,7 @@ Accessing biases:\n\
		}
		return COLVARSCRIPT_OK;
		} else {
		result = "Wrong arguments to command \"list\"";
		result = "Wrong arguments to command \"list\"\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		}
		@@ -125,12 +87,13 @@ Accessing biases:\n\
		/// Parse config from file
		if (cmd == "configfile") {
		if (argc < 3) {
		result = "Missing arguments";
		result = "Missing arguments\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		if (colvars->read_config_file(argv[2]) == COLVARS_OK) {
		return COLVARSCRIPT_OK;
		} else {
		result = "Error parsing configuration file";
		return COLVARSCRIPT_ERROR;
		}
		}
		@@ -138,13 +101,14 @@ Accessing biases:\n\
		/// Parse config from string
		if (cmd == "config") {
		if (argc < 3) {
		result = "Missing arguments";
		result = "Missing arguments\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		std::string conf = argv[2];
		if (colvars->read_config_string(conf) == COLVARS_OK) {
		return COLVARSCRIPT_OK;
		} else {
		result = "Error parsing configuration string";
		return COLVARSCRIPT_ERROR;
		}
		}
		@@ -152,13 +116,14 @@ Accessing biases:\n\
		/// Load an input state file
		if (cmd == "load") {
		if (argc < 3) {
		result = "Missing arguments";
		result = "Missing arguments\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		proxy->input_prefix_str = argv[2];
		if (colvars->setup_input() == COLVARS_OK) {
		return COLVARSCRIPT_OK;
		} else {
		result = "Error loading state file";
		return COLVARSCRIPT_ERROR;
		}
		}
		@@ -197,27 +162,28 @@ Accessing biases:\n\
		result = cvm::to_str(f);
		return COLVARSCRIPT_OK;
		} else {
		result = "Wrong arguments to command \"frame\"";
		result = "Wrong arguments to command \"frame\"\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		}

		result = "Syntax error";
		result = "Syntax error\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}


		int colvarscript::proc_colvar(int argc, char const *argv[]) {
		if (argc < 3) {
		result = "Missing parameters\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}

		std::string name = argv[1];
		colvar *cv = cvm::colvar_by_name(name);
		if (cv == NULL) {
		result = "Colvar not found: " + name;
		return COLVARSCRIPT_ERROR;
		}
		if (argc < 3) {
		result = "Missing parameters";
		return COLVARSCRIPT_ERROR;
		}
		std::string subcmd = argv[2];

		if (subcmd == "value") {
		@@ -261,7 +227,7 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {

		if (subcmd == "addforce") {
		if (argc < 4) {
		result = "addforce: missing parameter: force value";
		result = "addforce: missing parameter: force value\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		std::string f_str = argv[3];
		@@ -279,12 +245,17 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
		return COLVARSCRIPT_OK;
		}

		result = "Syntax error";
		result = "Syntax error\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}


		int colvarscript::proc_bias(int argc, char const *argv[]) {
		if (argc < 3) {
		result = "Missing parameters\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}

		std::string name = argv[1];
		colvarbias *b = cvm::bias_by_name(name);
		if (b == NULL) {
		@@ -292,10 +263,6 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
		return COLVARSCRIPT_ERROR;
		}

		if (argc < 3) {
		result = "Missing parameters";
		return COLVARSCRIPT_ERROR;
		}
		std::string subcmd = argv[2];

		if (subcmd == "energy") {
		@@ -362,9 +329,55 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
		return COLVARSCRIPT_OK;
		}

		result = "Syntax error";
		result = "Syntax error\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}
		result = "Syntax error";

		result = "Syntax error\n" + help_string();
		return COLVARSCRIPT_ERROR;
		}


		std::string colvarscript::help_string()
		{
		std::string buf;
		buf = "Usage: cv <subcommand> [args...]\n\
		\n\
		Managing the colvars module:\n\
		configfile <file name> -- read configuration from a file\n\
		config <string> -- read configuration from the given string\n\
		reset -- delete all internal configuration\n\
		delete -- delete this colvars module instance\n\
		version -- return version of colvars code\n\
		\n\
		Input and output:\n\
		list -- return a list of all variables\n\
		list biases -- return a list of all biases\n\
		load <file name> -- load a state file (requires configuration)\n\
		update -- recalculate colvars and biases based\n\
		printframe -- return a summary of the current frame\n\
		printframelabels -- return labels to annotate printframe's output\n";

		if (proxy->frame() != COLVARS_NOT_IMPLEMENTED) {
		buf += "\
		frame -- return current frame number\n\
		frame <new_frame> -- set frame number\n";
		}

		buf += "\n\
		Accessing collective variables:\n\
		colvar <name> value -- return the current value of colvar <name>\n\
		colvar <name> update -- recalculate colvar <name>\n\
		colvar <name> type -- return the type of colvar <name>\n\
		colvar <name> delete -- delete colvar <name>\n\
		colvar <name> addforce <F> -- apply given force on colvar <name>\n\
		colvar <name> getconfig -- return config string of colvar <name>\n\
		\n\
		Accessing biases:\n\
		bias <name> energy -- return the current energy of bias <name>\n\
		bias <name> update -- recalculate bias <name>\n\
		bias <name> delete -- delete bias <name>\n\
		bias <name> getconfig -- return config string of bias <name>\n";

		return buf;
		}

lib/colvars/colvarscript.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -36,11 +36,15 @@ public:
		/// Run script command with given positional arguments
		int run(int argc, char const *argv[]);

		private:
		/// Run subcommands on colvar
		int proc_colvar(int argc, char const *argv[]);

		/// Run subcommands on bias
		int proc_bias(int argc, char const *argv[]);

		/// Builds and return a short help
		std::string help_string(void);
		};

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