final touches to support compiling with libcurl transparently (741a7fe6) · Commits · 郑智淋 / lammps

examples/kim/in.query

0 → 100644

+11 −0

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		# example for performing a query to the OpenKIM test database to retrieve
		# a parameter to be used in the input. here it requests the aluminium
		# lattice constant for a specific test used for a specific model and then
		# assigns it to the variable 'latconst'

		units metal
		info variables out log
		kim_query latconst get_test_result test=TE_156715955670_004 species=["Al"] model=MO_800509458712_001 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
		info variables out log
		lattice fcc ${latconst}

examples/kim/log.16Aug2018.query.g++.1

0 → 100644

+34 −0

Original line number	Diff line number	Diff line
		LAMMPS (16 Aug 2018)

		# example for performing a query to the OpenKIM test database to retrieve
		# a parameter to be used in the input. here it requests the aluminium
		# lattice constant for a specific test used for a specific model and then
		# assigns it to the variable 'latconst'

		units metal
		info variables out log

		Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
		Printed on Mon Aug 20 18:44:24 2018


		Variable information:

		Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info

		kim_query latconst get_test_result test=TE_156715955670_004 species=["Al"] model=MO_800509458712_001 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
		info variables out log

		Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
		Printed on Mon Aug 20 18:44:24 2018


		Variable information:
		Variable[ 0]: latconst , style = string , def = 4.0320827961

		Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info

		lattice fcc ${latconst}
		lattice fcc 4.0320827961
		Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
		Total wall time: 0:00:00

lib/kim/Makefile.lammps

+6 −1

Original line number	Diff line number	Diff line
		@@ -17,13 +17,18 @@
		ifeq ($(strip $(shell pkg-config --version)),)
		$(error 'pkg-config' not found, but is required to configure the KIM API)
		endif

		kim_PREFIX := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null)
		kim_PREFIX := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,)
		kim_PREFIX := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX))

		# there is no usable libcurl installation
		ifeq ($(shell curl-config --version 2> /dev/null),)
		kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null)
		kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null)
		else
		kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null) $(shell curl-config --cflags) -DLMP_KIM_CURL
		kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null) $(shell curl-config --libs)
		endif

		ifeq ($(strip $(kim_SYSINC)),)
		$(error 'pkg-config' could not find an installed KIM API library.)

lib/kim/README

+6 −0

Original line number	Diff line number	Diff line
		@@ -13,6 +13,12 @@ do the same thing by typing "python Install.py" from within this
		directory, or you can do it manually by following the instructions
		below.

		As of KIM API version 2, the KIM package also provides a LAMMPS command
		to perform queries through the OpenKIM web API. This feature requires
		that the CURL library (libcurl) development package and its configuration
		query tool, curl-config, are installed. The provided Makefile.lammps
		is set up to automatically detect this.

		-----------------

		Instructions:

src/KIM/kim_query.cpp

+134 −22

Original line number	Diff line number	Diff line
		@@ -57,36 +57,55 @@

		#include <mpi.h>
		#include <cstring>
		#include <string>
		#include "kim_query.h"
		#include "comm.h"
		#include "error.h"
		#include "input.h"
		#include "variable.h"

		#include <sys/types.h>
		#include <curl/curl.h>

		using namespace LAMMPS_NS;

		static char do_query(char , char *, int, MPI_Comm);
		#if defined(LMP_KIM_CURL)

		struct WriteBuf {
		char *dataptr;
		size_t sizeleft;
		};

		static char do_query(char , int, char **, int, MPI_Comm);
		static size_t write_callback(void , size_t, size_t, void );

		#endif

		/* ---------------------------------------------------------------------- */

		void KimQuery::command(int narg, char **arg)
		{
		char model, property, varname, value;
		char varname, function, *value;

		if (narg < 2) error->all(FLERR,"Illegal kim_query command");

		if (narg != 3) error->all(FLERR,"Illegal kim_query command");
		varname = arg[0];
		function = arg[1];

		model = arg[0];
		property = arg[1];
		varname = arg[2];
		#if defined(LMP_KIM_CURL)

		value = do_query(model, property, comm->me, world);
		value = do_query(function, narg-2, arg+2, comm->me, world);

		// check for valid result
		// on error the content of "value" is a '\0' byte
		// as the first element, and then the error message
		// that was returned by the web server

		int len = strlen(value) + 1;
		if (len == 1) {
		// TODO: store more detailed error message after \0 byte.
		error->all(FLERR,"Query of OpenKIM database failed");
		if (0 == strlen(value)) {
		char errmsg[512];

		sprintf(errmsg,"OpenKIM query failed: %s",value+1);
		error->all(FLERR,errmsg);
		}

		char *varcmd = new char[3];
		@@ -98,26 +117,119 @@ void KimQuery::command(int narg, char **arg)

		delete[] varcmd;
		delete[] value;
		#else
		error->all(FLERR,"Cannot use 'kim_query' command when KIM package "
		"is compiled without support for libcurl");
		#endif
		}

		#if defined(LMP_KIM_CURL)

		// copy data to the user provided data structure, optionally in increments

		size_t write_callback(void data, size_t size, size_t nmemb, void userp)
		{
		struct WriteBuf buf = (struct WriteBuf )userp;
		size_t buffer_size = size*nmemb;

		// copy chunks into the buffer for as long as there is space left
		if (buf->sizeleft) {
		size_t copy_this_much = buf->sizeleft;
		if (copy_this_much > buffer_size)
		copy_this_much = buffer_size;
		memcpy(buf->dataptr, data, copy_this_much);

		buf->dataptr += copy_this_much;
		buf->sizeleft -= copy_this_much;
		return copy_this_much;
		}
		return 0; // done
		}

		char do_query(char model, char *property, int rank, MPI_Comm comm)
		char do_query(char qfunction, int narg, char **arg, int rank, MPI_Comm comm)
		{
		char value[512], *retval;

		// only run query from rank 0
		// run the web query from rank 0 only

		if (rank == 0) {
		CURL *handle;
		CURLcode res;

		// set up and clear receive buffer

		struct WriteBuf buf;
		buf.dataptr = value;
		buf.sizeleft = 511;
		memset(value,0,512);

		// create curl web query instance
		curl_global_init(CURL_GLOBAL_DEFAULT);
		handle = curl_easy_init();

		if (handle) {
		std::string url("https://query.openkim.org/api/");
		url += qfunction;

		std::string query(arg[0]);
		for (int i=1; i < narg; ++i) {
		query += '&';
		query += arg[i];
		}

		// fake query
		strcpy(value,(const char*)"4.25");
		#if LMP_DEBUG_CURL
		curl_easy_setopt(handle, CURLOPT_VERBOSE, 1L);
		#endif

		#if defined(LMP_NO_SSL_CHECK)
		// disable verifying SSL certificate and host name
		curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L);
		curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L);
		#endif

		curl_easy_setopt(handle, CURLOPT_URL, url.c_str());
		curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L);
		curl_easy_setopt(handle, CURLOPT_POSTFIELDS, query.c_str());

		curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION,write_callback);
		curl_easy_setopt(handle, CURLOPT_WRITEDATA,&buf);

		// perform OpenKIM query and check for errors
		res = curl_easy_perform(handle);
		if (res != CURLE_OK) {
		// on error we return an "empty" string but add error message after it
		value[0]= '\0';
		strcpy(value+1,curl_easy_strerror(res));
		}
		curl_easy_cleanup(handle);
		}
		curl_global_cleanup();
		}
		MPI_Bcast(value, 512, MPI_CHAR, 0, comm);

		// must make a proper copy of the query, as the stack allocation
		// will go out of scope
		// we must make a proper copy of the query, as the stack allocation
		// for "value" will go out of scope. a valid query has a '[' as
		// the first character. skip over it (and the last character ']', too)
		// an error messages starts with a '\0' character. copy that and
		// the remaining string, as that is the error message.

		if (value[0] == '[') {
		int len = strlen(value)-1;
		retval = new char[len];
		value[len] = '\0';
		strcpy(retval,value+1);
		} else if (value[0] == '\0') {
		int len = strlen(value+1)+2;
		retval = new char[len];
		retval[0] = '\0';
		strcpy(retval+1,value+1);
		} else {
		// unknown response type. we should not get here.
		// copy response without modifications.
		int len = strlen(value)+1;
		retval = new char[len];
		strcpy(retval,value);
		}
		return retval;
		}
		#endif

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