Merge pull request #863 from ellio167/kim-update

KIM API interface update

cmake/CMakeLists.txt

@@ -290,7 +290,21 @@ if(ENABLE_USER-VTK)
 endif()
 
 if(ENABLE_KIM)
-  find_package(KIM REQUIRED)
+  find_package(KIM QUIET)
+  if(NOT KIM_FOUND)
+    message(STATUS "KIM not found - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(kim_build
+      URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz
+      URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+      )
+    ExternalProject_get_property(kim_build INSTALL_DIR)
+    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
+    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
+    list(APPEND LAMMPS_DEPS kim_build)
+  endif()
   list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
   include_directories(${KIM_INCLUDE_DIRS})
 endif()

lib/kim/Install.py

@@ -21,7 +21,7 @@ Syntax from lib dir: python Install.py -b -v version  -a kim-name
 specify one or more options, order does not matter
 
   -v = version of KIM API library to use
-       default = kim-api-v1.9.2 (current as of Oct 2017)
+       default = kim-api-v1.9.4 (current as of Apr 2018)
   -b = download and build base KIM API library with example Models
        this will delete any previous installation in the current folder
   -n = do NOT download and build base KIM API library.
@@ -109,7 +109,7 @@ nargs = len(args)
 if nargs == 0: error()
 
 thisdir = os.environ['PWD']
-version = "kim-api-v1.9.2"
+version = "kim-api-v1.9.4"
 
 buildflag = False
 everythingflag = False
@@ -166,9 +166,6 @@ if pathflag:
     mkfile.write("print_dir:\n")
     mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
 
-  with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
-    cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
-
   print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
 else:
   kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
@@ -191,9 +188,6 @@ if buildflag:
     mkfile.write("print_dir:\n")
     mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
 
-  with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
-    cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
-
   print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
 
   # download entire kim-api tarball
@@ -247,11 +241,16 @@ if buildflag:
 # add single OpenKIM model
 if addflag:
 
+  makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR")
+  if os.path.isfile(makefile_path):
+    cmd = 'make --no-print-directory -f %s print_dir' % makefile_path
+    kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+
   if not os.path.isdir(kimdir):
     print("\nkim-api is not installed")
     error()
 
   # download single model
-  cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir, addmodelname)
+  cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
   txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
   if verboseflag: print (txt.decode("UTF-8"))

lib/kim/README

@@ -20,47 +20,35 @@ Instructions:
 
 1. Configure lammps for use with the kim-api library installed in this directory
 
-$ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR
-$ printf "include ${PWD}/lib/kim-api/Makefile.KIM_Config\n" > ./Makefile.KIM_Config
+# replace X.Y.Z as appropriate here and below
+$ printf "KIM_INSTALL_DIR=${PWD}/installed-kim-api-vX.Y.Z\n" > ./Makefile.KIM_DIR
 
 2. Download and unpack the kim-api
 
-# replace X.Y.Z as appropriate here and below
-$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.tgz
-$ tar zxvf kim-api-vX.Y.Z.tgz
+$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.txz
+$ tar zxvf kim-api-vX.Y.Z.txz
 
 # configure the kim-api
 $ cd kim-api-vX.Y.Z
-$ ./configure --prefix=${PWD}/../
-
-# setup the desired kim item
-$ make add-Pair_Johnson_Fe__MO_857282754307_002
+$ ./configure --prefix=${PWD}/../installed-kim-api-vX.Y.Z
 
 3. Build and install the kim-api and model
 
 $ make
 $ make install
-
-# replace X with the KIM API major version number
-$ make install-set-default-to-vX
-$ cd ../
+$ cd ..
 
 4. Remove source and build files
 
 $ rm -rf kim-api-vX.Y.Z
-$ rm -rf kim-api-vX.Y.Z.tgz
+$ rm -rf kim-api-vX.Y.Z.txz
 
-5. To add additional items do the following (replace the kim item name with your
+5. To add items do the following (replace the kim item name with your
    desired value)
 
-$ wget https://openkim.org/download/EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
-$ tar zxvf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
-$ cd EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001
-$ make
-$ make install
-$ cd ..
-$ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001
-$ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
+$ source ${PWD}/kim-api-vX.Y.Z/bin/kim-api-v1-activate
+$ kim-api-v1-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
+
 
 -----------------
 
@@ -73,4 +61,4 @@ $ make g++ (or whatever target you wish)
 
 Note that the Makefile.lammps and Makefile.KIM_DIR files in this directory
 are required to allow the LAMMPS build to find the necessary KIM files.
-You should not normally need to edit this file.
+You should not normally need to edit these files.

lib/kim/pair-kim.release.info

-This package (pair-kim-v1.7.2+1) created from commit
-
-ced1275c5fd5b382cb9bd39e44ed1324c7c85e99
-
-of the pair-kim git repository
-By Ryan S. Elliott (relliott@umn.edu) on Mon Feb 22 14:59:53 CST 2016.

src/KIM/pair_kim.cpp

@@ -27,7 +27,6 @@
 
 // includes from LAMMPS
 #include "pair_kim.h"
-#include "pair_kim_version.h"
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
@@ -1094,18 +1093,6 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
       "#\n"
       "# This file is automatically generated from LAMMPS pair_style "
           "kim command\n");
-   char tmp_version[100];
-   sprintf(tmp_version,"# This is pair-kim-v%i.%i.%i",
-           PAIR_KIM_VERSION_MAJOR, PAIR_KIM_VERSION_MINOR,
-           PAIR_KIM_VERSION_PATCH);
-   strcat(*test_descriptor_string, tmp_version);
-#ifdef PAIR_KIM_VERSION_PRERELEASE
-   sprintf(tmp_version,"-%s", PAIR_KIM_VERSION_PRERELEASE);
-   strcat(*test_descriptor_string, tmp_version);
-#endif
-#ifdef PAIR_KIM_VERSION_BUILD_METADATA
-   sprintf(tmp_version,"+%s", PAIR_KIM_VERSION_BUILD_METADATA);
-#endif
    strcat(*test_descriptor_string,
       "\n"
       "# The call number is (pair_style).(init_style): ");

src/KIM/pair_kim_version.h

-/* -*- 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: Ryan S. Elliott,
-------------------------------------------------------------------------- */
-
-#ifndef LMP_PAIR_KIM_VERSION_H
-#define LMP_PAIR_KIM_VERSION_H
-
-//
-// Release: This file is part of the pair-kim-v1.7.2+1 package.
-//
-
-//
-// This file defines the version information for the pair-kim package.
-// The values specified here must conform to the Semantic Versioning
-// 2.0.0 specification.
-//
-// Generally the version numbering for the pair-kim package will
-// parallel the numbering for the kim-api package.  However, if
-// additional versioning increments are required for the pair-kim
-// package, the build-metatdata field will be used to provide a
-// "sub-patch" version number.
-//
-// The PATCH value should be incremented IMMEDIATELY after an official
-// release.
-//
-// The MINOR value should be incremented AND the PATCH value reset to
-// zero as soon as it becomes clear that the next official release
-// MUST increment the MINOR version value.
-//
-// The MAJOR value should be incremented AND the MINOR and PATCH
-// vaules reset to zero as soon as it becomes clear that the next
-// official release MUST increment the MAJOR version value.
-//
-// The PRERELEASE value can be set to any value allowed by the
-// Semantic Versioning specification.  However, it will generally be
-// empty.  This value should be quoted as a string constant.
-//
-// The BUILD_METADATA value can be set to any value allowed by the
-// Semantic Versioning specification.  However, it will generally be
-// emtpy; Except for when "sub-patch" versioning of the pair-kim
-// package is necessary.  This value should be quoted as a string
-// constant.
-//
-
-#define PAIR_KIM_VERSION_MAJOR 1
-#define PAIR_KIM_VERSION_MINOR 7
-#define PAIR_KIM_VERSION_PATCH 2
-//#define PAIR_KIM_VERSION_PRERELEASE
-#define PAIR_KIM_VERSION_BUILD_METADATA "1"
-
-#endif  /* PAIR_KIM_VERSION_H */

src/Purge.list

@@ -16,6 +16,8 @@ style_region.h
 style_neigh_bin.h
 style_neigh_pair.h
 style_neigh_stencil.h
+# deleted on 4 April 2018
+pair_kim_version.h
 # deleted on 15 December 2017
 fix_python.cpp
 fix_python.h