Merge branch 'kim-simulator-models' of github.com:ellio167/lammps into kim-simulator-models (358cec9a) · Commits · 郑智淋 / lammps

doc/src/kim_commands.txt

+9 −5

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657
		kim_interactions C H O
		kim_init Sim_LAMMPS_IFF_OtherInfo_AuthorList_Year_Species__SM_064312669787_000 real
		kim_interactions fixed_types
		kim_query a0 get_lattice_constant_fcc species=\["Al"] units=\["angstrom"\] :pre
		kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] :pre


		[Description:]
		@@ -105,12 +105,16 @@ The URL for such a page is constructed from the
		"extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM:

		https://openkim.org/id/extended_KIM_ID
		or
		https://openkim.org/id/short_KIM_ID
		:pre

		For example for the Stillinger-Weber potential
		listed above the Model Page is located at:

		"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005
		or
		"https://openkim.org/id/MO_405512056662_005"_https://openkim.org/id/MO_405512056662_005
		:pre

		See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species.
		@@ -271,8 +275,8 @@ OpenKIM IM Execution ({kim_interactions}) :h5

		The second and final step in using an OpenKIM IM is to execute the
		{kim_interactions} command. This command must be preceded by a {kim_init}
		command and a "create_box"_create_box.html command,
		which defines the number of atom types {N}.
		command and a command that creates the simulation box (such as
		"create_box"_create_box.html), which defines the number of atom types {N}.
		The {kim_interactions} command has one argument {typeargs}. This argument
		contains either a list of {N} chemical species, which defines a mapping between
		atom types in LAMMPS to the available species in the OpenKIM IM, or the
		@@ -338,7 +342,7 @@ Note also that parameters like cutoff radii and charge tolerances,
		which have an effect on IM predictions, are also included in the
		SM definition ensuring reproducibility.

		NOTE: When using using {kim_init} and {kim_interactions} to select
		NOTE: When using {kim_init} and {kim_interactions} to select
		and set up an OpenKIM IM, other LAMMPS commands
		for the same functions (such as pair_style, pair_coeff, bond_style,
		bond_coeff, fixes related to charge equilibration, etc.) should normally
		@@ -356,7 +360,7 @@ argument of the {kim_query command}. The second required argument
		(e.g. {get_lattice_constant_fcc}).
		All following arguments are parameters handed over to the web query
		in the format {keyword=value}. The list of supported keywords and
		and the type and format of their values depend on the query function
		the type and format of their values depend on the query function
		used.

		NOTE: The current list of supported query functions is available on the OpenKIM

src/KIM/kim_query.cpp

+16 −7

Original line number	Diff line number	Diff line
		@@ -124,7 +124,7 @@ void KimQuery::command(int narg, char **arg)
		// that was returned by the web server

		if (0 == strlen(value)) {
		char errmsg[512];
		char errmsg[1024];

		sprintf(errmsg,"OpenKIM query failed: %s",value+1);
		error->all(FLERR,errmsg);
		@@ -138,6 +138,8 @@ void KimQuery::command(int narg, char **arg)
		varcmd[1] = (char *) "string";

		while(std::getline(ss, token, ',')) {
		token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim
		token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim
		std::stringstream splitname;
		splitname << varname << "_" << counter++;
		varcmd[0] = const_cast<char *>(splitname.str().c_str());
		@@ -256,9 +258,15 @@ char do_query(char qfunction, char * model_name, int narg, char **arg,

		if (value[0] == '[') {
		int len = strlen(value)-1;
		if (value[len-1] == ']') {
		retval = new char[len];
		value[len] = '\0';
		value[len-1] = '\0';
		strcpy(retval,value+1);
		} else {
		retval = new char[len+2];
		retval[0] = '\0';
		strcpy(retval+1,value);
		}
		} else if (value[0] == '\0') {
		int len = strlen(value+1)+2;
		retval = new char[len];
		@@ -266,10 +274,11 @@ char do_query(char qfunction, char * model_name, int narg, char **arg,
		strcpy(retval+1,value+1);
		} else {
		// unknown response type. we should not get here.
		// copy response without modifications.
		int len = strlen(value)+1;
		// we return an "empty" string but add error message after it
		int len = strlen(value)+2;
		retval = new char[len];
		strcpy(retval,value);
		retval[0] = '\0';
		strcpy(retval+1,value);
		}
		return retval;
		}

Admin message