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Merge pull request #1371 from akohlmey/add-kim-query

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Add kim_query command to KIM package
This commit is contained in:
Axel Kohlmeyer
2019-03-25 13:15:20 -04:00
committed by GitHub
parent 1bd47f0318 d5074b39a0
commit 5d54e888d5
16 changed files with 450 additions and 15 deletions
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6
cmake/CMakeLists.txt
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@ -670,6 +670,12 @@ if(PKG_USER-VTK)
endif()
if(PKG_KIM)
find_package(CURL)
if(CURL_FOUND)
include_directories(${CURL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
add_definitions(-DLMP_KIM_CURL)
endif()
option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
if(DOWNLOAD_KIM)
message(STATUS "KIM-API v2 download requested - we will build our own")

14
doc/src/Build_extras.txt
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@ -169,16 +169,18 @@ used to build the GPU library.
KIM package :h4,link(kim)
To build with this package, the KIM library must be downloaded and
built on your system. It must include the KIM models that you want to
use with LAMMPS.
To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS. If you want to use the "kim_query"_kim_query.html
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
Note that in LAMMPS lingo, a KIM model driver is a pair style
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
element or alloy and set of parameters, e.g. EAM for Cu with a
specific EAM potential file. Also note that installing the KIM API
library with all its models, may take around 30 min to build. Of
course you only need to do that once.
specific EAM potential file. Also note that downloading and installing
the KIM API library with all its models, may take a long time (10s of
minutes to hours) to build. Of course you only need to do that once.
See the list of KIM model drivers here:
https://openkim.org/browse/model-drivers/alphabetical

1
doc/src/Commands_all.txt
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@ -68,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kim_query"_kim_query.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,

2
doc/src/Packages_details.txt
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@ -341,6 +341,8 @@ KIM package :link(PKG-KIM),h4
A "pair_style kim"_pair_kim.html command which is a wrapper on the
Knowledge Base for Interatomic Models (KIM) repository of interatomic
potentials, enabling any of them to be used in LAMMPS simulations.
Also a "kim_query"_kim_query.html command, which allows to query
the OpenKIM database for stored properties.
To use this package you must have the KIM library available on your
system.

1
doc/src/commands_list.txt
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@ -53,6 +53,7 @@ Commands :h1
include
info
jump
kim_query
kspace_modify
kspace_style
label

45
doc/src/kim_query.txt Normal file
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@ -0,0 +1,45 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
kim_query command :h3
[Syntax:]
kim_query variable query_function web_query_flags :pre
variable = name of a (string style) variable where the result of the query is stored
query_function = name of the OpenKIM web API query function to be used
web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
[Examples:]
kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
[Description:]
The kim_query command allows to retrieve properties from the OpenKIM
through a web query. The result is stored in a string style
"variable"_variable.html, the name of which must be given as the first
argument of the kim_query command. The second required argument is the
name of the actual query function (e.g. {get_test_result}). All following
arguments are parameters handed over to the web query in the format
{keyword=value}. This list of supported keywords and the type of how
the value has to be encoded depends on the query function used.
For more details on this, please refer to the OpenKIM homepage.
[Restrictions:]
This command is part of the KIM package. It is only enabled if
LAMMPS was built with that package. Furthermore, its correct
functioning depends on compiling LAMMPS with libcurl support.
See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
"pair_style kim"_pair_kim.html, "variable"_variable.html

1
doc/src/lammps.book
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@ -167,6 +167,7 @@ if.html
include.html
info.html
jump.html
kim_query.html
label.html
lattice.html
log.html

9
doc/src/pair_kim.txt
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@ -42,12 +42,9 @@ section of the "Packages details"_Packages_details.html doc page has
instructions on how to do this with a simple make command, when
building LAMMPS.
See the examples/kim dir for an input script that uses a KIM model (potential)
for Lennard-Jones. Note, for this example input script, the example models
shipped with with kim-api package must be installed. See the "Build
package"_Build_package.html section and the ./lib/kim/README for details
on how to build LAMMSPS with the kim-api and how to install the example models.
See the examples/kim dir for an input script that uses a KIM model
(potential) for Lennard-Jones.
:line
The argument {model} is the name of the KIM model for a specific

1
doc/utils/sphinx-config/false_positives.txt
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@ -1382,6 +1382,7 @@ libAtoms
libawpmd
libch
libcolvars
libcurl
libdir
libdl
libfftw

11
examples/kim/in.query Normal file
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@ -0,0 +1,11 @@
# 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 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
info variables out log
lattice fcc ${latconst}

34
examples/kim/log.22Mar2019.query.g++.1 Normal file
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@ -0,0 +1,34 @@
LAMMPS (28 Feb 2019)
# 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 Fri Mar 22 20:00:56 2019
Variable information:
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 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 Fri Mar 22 20:00:57 2019
Variable information:
Variable[ 0]: latconst , style = string , def = 4.03208274841
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
lattice fcc ${latconst}
lattice fcc 4.03208274841
Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
Total wall time: 0:00:00

7
lib/kim/Makefile.lammps
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@ -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.)

6
lib/kim/README
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@ -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:

7
src/.gitignore vendored
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@ -26,6 +26,11 @@
/*_ssa.h
/*_ssa.cpp
/kim_query.cpp
/kim_query.h
/pair_kim.cpp
/pair_kim.h
/kokkos.cpp
/kokkos.h
/kokkos_type.h
@ -818,8 +823,6 @@
/pair_hbond_dreiding_morse.h
/pair_ilp_graphene_hbn.cpp
/pair_ilp_graphene_hbn.h
/pair_kim.cpp
/pair_kim.h
/pair_kolmogorov_crespi_full.cpp
/pair_kolmogorov_crespi_full.h
/pair_kolmogorov_crespi_z.cpp

235
src/KIM/kim_query.cpp Normal file
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@ -0,0 +1,235 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2 of the License, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <https://www.gnu.org/licenses>.
Linking LAMMPS statically or dynamically with other modules is making a
combined work based on LAMMPS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
In addition, as a special exception, the copyright holders of LAMMPS give
you permission to combine LAMMPS with free software programs or libraries
that are released under the GNU LGPL and with code included in the standard
release of the "kim-api" under the CDDL (or modified versions of such code,
with unchanged license). You may copy and distribute such a system following
the terms of the GNU GPL for LAMMPS and the licenses of the other code
concerned, provided that you include the source code of that other code
when and as the GNU GPL requires distribution of source code.
Note that people who make modified versions of LAMMPS are not obligated to
grant this special exception for their modified versions; it is their choice
whether to do so. The GNU General Public License gives permission to release
a modified version without this exception; this exception also makes it
possible to release a modified version which carries forward this exception.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the kim-api-v2-2.0.0 (and newer) package
------------------------------------------------------------------------- */
#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;
#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 *varname, *function, *value;
if (narg < 2) error->all(FLERR,"Illegal kim_query command");
varname = arg[0];
function = arg[1];
#if defined(LMP_KIM_CURL)
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
if (0 == strlen(value)) {
char errmsg[512];
sprintf(errmsg,"OpenKIM query failed: %s",value+1);
error->all(FLERR,errmsg);
}
char **varcmd = new char*[3];
varcmd[0] = varname;
varcmd[1] = (char *) "string";
varcmd[2] = value;
input->variable->set(3,varcmd);
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 *qfunction, int narg, char **arg, int rank, MPI_Comm comm)
{
char value[512], *retval;
// 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];
}
#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);
// 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

85
src/KIM/kim_query.h Normal file
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@ -0,0 +1,85 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2 of the License, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <https://www.gnu.org/licenses>.
Linking LAMMPS statically or dynamically with other modules is making a
combined work based on LAMMPS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
In addition, as a special exception, the copyright holders of LAMMPS give
you permission to combine LAMMPS with free software programs or libraries
that are released under the GNU LGPL and with code included in the standard
release of the "kim-api" under the CDDL (or modified versions of such code,
with unchanged license). You may copy and distribute such a system following
the terms of the GNU GPL for LAMMPS and the licenses of the other code
concerned, provided that you include the source code of that other code
when and as the GNU GPL requires distribution of source code.
Note that people who make modified versions of LAMMPS are not obligated to
grant this special exception for their modified versions; it is their choice
whether to do so. The GNU General Public License gives permission to release
a modified version without this exception; this exception also makes it
possible to release a modified version which carries forward this exception.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the kim-api-v2-2.0.0 (and newer) package
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(kim_query,KimQuery)
#else
#ifndef LMP_KIM_QUERY_H
#define LMP_KIM_QUERY_H
#include "pointers.h"
namespace LAMMPS_NS {
class KimQuery : protected Pointers {
public:
KimQuery(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/