[pull] develop from lammps:develop

cmake/Modules/Packages/KIM.cmake

@@ -27,11 +27,23 @@ endif()
 option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
 if(DOWNLOAD_KIM)
   message(STATUS "KIM-API download requested - we will build our own")
+  if(NOT KIM-API_FOUND)
+      message(WARNING "KIM-API was not found, and DOWNLOAD_KIM is on, "
+              "so we will download and build our own. "
+              "If you intend to use LAMMPS with a pre-installed KIM-API, "
+              "you may need to set PKG_CONFIG_PATH, or run the command "
+              "'source kim-api-activate', then re-run CMake.")
+  else()
+      message(WARNING "KIM-API was was found, but DOWNLOAD_KIM is on, "
+              "so we will download and build our own. If you intend "
+              "to use LAMMPS with your pre-installed KIM-API, you "
+              "should disable DOWNLOAD_KIM and re-run CMake.")
+  endif()
   include(ExternalProject)
   enable_language(C)
   enable_language(Fortran)
-  set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball")
-  set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball")
+  set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.4.2.txz" CACHE STRING "URL for KIM tarball")
+  set(KIM_MD5 "bd51faa7edfaab437047aea0c25a5dfb" CACHE STRING "MD5 checksum of KIM tarball")
   mark_as_advanced(KIM_URL)
   mark_as_advanced(KIM_MD5)
   ExternalProject_Add(kim_build

doc/src/Build_extras.rst

@@ -386,9 +386,12 @@ option in preparations to run on Aurora system at Argonne.
 KIM package
 ---------------------
 
-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.
+To build with this package, the KIM API v2.0+ must be downloaded
+and built on your system. See
+`Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
+learn how to install the KIM API, as well as how to install any models you
+wish to use afterward.
+See the list of all KIM models here: https://openkim.org/browse/models
 
 If you would like to use the :doc:`kim query <kim_commands>`
 command, you also need to have libcurl installed with the matching
@@ -404,16 +407,6 @@ channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
 detailed information is available at:
 `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 
-In addition to installing the KIM API, it is also necessary to install the
-library of KIM models (interatomic potentials).
-See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
-learn how to install a pre-build binary of the OpenKIM Repository of Models.
-See the list of all KIM models here: https://openkim.org/browse/models
-
-(Also note that when downloading and installing from source
-the KIM API library with all its models, may take a long time (tens of
-minutes to hours) to build.  Of course you only need to do that once.)
-
 .. tabs::
 
    .. tab:: CMake build
@@ -430,11 +423,15 @@ minutes to hours) to build.  Of course you only need to do that once.)
                                          # value = no (default) or yes
 
       If ``DOWNLOAD_KIM`` is set to ``yes`` (or ``on``), the KIM API library
-      will be downloaded and built inside the CMake build directory.  If
+      will be downloaded and built inside the CMake build directory.  Note that
+      in most cases it is recommended that you do not use this option, and instead
+      provide a KIM API installation yourself before building LAMMPS.  If
       the KIM library is already installed on your system (in a location
       where CMake cannot find it), you may need to set the
       ``PKG_CONFIG_PATH`` environment variable so that libkim-api can be
-      found, or run the command ``source kim-api-activate``.
+      found, or run the command ``source kim-api-activate``.  If CMake cannot find
+      the KIM API when configuring for the first time (or after clearing the
+      CMake cache), the default value of the ``DOWNLOAD_KIM`` option will be ``yes``.
 
       Extra unit tests can only be available if they are explicitly requested
       (``KIM_EXTRA_UNITTESTS`` is set to ``yes`` (or ``on``)) and the prerequisites
@@ -495,9 +492,9 @@ Enabling the extra unit tests have some requirements,
   `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 * It is also necessary to install the following KIM models:
 
-  * ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``
-  * ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``
-  * ``LennardJones612_UniversalShifted__MO_959249795837_003``
+  * ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_001``
+  * ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_006``
+  * ``LennardJones612_UniversalShifted__MO_959249795837_003`` (this model is an example model automatically built with the API unless explicitly disabled)
 
   See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
   to learn how to install a pre-built binary of the OpenKIM Repository of

doc/src/kim_commands.rst

@@ -416,7 +416,8 @@ Using OpenKIM Web Queries in LAMMPS (*kim query*)
 
 The *kim query* command performs a web query to retrieve the predictions of an
 IM set by *kim init* for material properties archived in
-`OpenKIM <https://openkim.org>`_.
+`OpenKIM <https://openkim.org>`_, or to obtain a list of available models
+that support a given set of atomic species.
 
 Syntax
 ------
@@ -483,6 +484,12 @@ and format of their values depend on the query function used.  The current list
 of query functions is available on the OpenKIM webpage at
 `https://openkim.org/doc/usage/kim-query <https://openkim.org/doc/usage/kim-query/>`_.
 
+.. note::
+
+   The *get_available_models* function's output is post-processed by LAMMPS so that
+   only the names of models that are currently installed are stored in the variable.
+   Matching models that are not installed are instead written to the LAMMPS log file.
+
 .. note::
 
    All query functions, except *get_available_models*, require the

unittest/commands/test_kim_commands.cpp

@@ -34,6 +34,8 @@ using LAMMPS_NS::utils::split_words;
 
 namespace LAMMPS_NS {
 using ::testing::StrEq;
+using ::testing::DoubleNear;
+using ::testing::Eq;
 
 class KimCommandsTest : public LAMMPSTest {
 protected:
@@ -577,14 +579,14 @@ TEST_F(KimCommandsTest, kim_query)
     command("clear");
     command("kim query latconst_1 get_lattice_constant_cubic "
             "crystal=[fcc] species=[Al] units=[angstrom] "
-            "model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]");
+            "model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_006]");
     END_HIDE_OUTPUT();
 
-    ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("4.032082033157349"));
+    ASSERT_THAT(std::stod(variable->retrieve("latconst_1")), DoubleNear(4.032082033157349, 1.e-2));
 
     BEGIN_HIDE_OUTPUT();
     command("clear");
-    command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal");
+    command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_006 metal");
     command("kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] "
             "units=[angstrom]");
 
@@ -593,50 +595,53 @@ TEST_F(KimCommandsTest, kim_query)
             "model=[LennardJones612_UniversalShifted__MO_959249795837_003]");
     END_HIDE_OUTPUT();
 
-    ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("4.032082033157349"));
-    ASSERT_THAT(variable->retrieve("latconst_2"), StrEq("3.328125931322575"));
+    ASSERT_THAT(std::stod(variable->retrieve("latconst_1")), DoubleNear(4.032082033157349, 1.e-2));
+    ASSERT_THAT(std::stod(variable->retrieve("latconst_2")), DoubleNear(3.328125931322575, 1.e-2));
 
     BEGIN_HIDE_OUTPUT();
     command("clear");
-    command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal");
+    command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_001 metal");
 
     command("kim query latconst split get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] "
             "units=[angstrom]");
     END_HIDE_OUTPUT();
 
-    ASSERT_THAT(variable->retrieve("latconst_1"), StrEq("3.234055244384789"));
-    ASSERT_THAT(variable->retrieve("latconst_2"), StrEq("5.167650199630013"));
+    ASSERT_THAT(std::stod(variable->retrieve("latconst_1")), DoubleNear(3.208725140430033, 1.e-2));
+    ASSERT_THAT(std::stod(variable->retrieve("latconst_2")), DoubleNear(5.239826212595919, 1.e-2));
 
     BEGIN_HIDE_OUTPUT();
     command("clear");
 
     command("kim query latconst index get_lattice_constant_hexagonal "
             "crystal=[hcp] species=[Zr] units=[angstrom] "
-            "model=[EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000]");
+            "model=[EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_001]");
     END_HIDE_OUTPUT();
-    ASSERT_THAT(variable->retrieve("latconst"), StrEq("3.234055244384789"));
+    ASSERT_THAT(std::stod(variable->retrieve("latconst")), DoubleNear(3.208725140430033, 1.e-2));
 
     BEGIN_HIDE_OUTPUT();
     command("variable latconst delete");
     command("clear");
-    command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal");
+    command("kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_001 metal");
 
     command("kim query latconst list get_lattice_constant_hexagonal crystal=[hcp] species=[Zr] "
             "units=[angstrom]");
     END_HIDE_OUTPUT();
 
-    ASSERT_THAT(variable->retrieve("latconst"), StrEq("3.234055244384789 5.167650199630013"));
+    std::vector<std::string> latconsts = utils::split_words(variable->retrieve("latconst"));
+    ASSERT_THAT(latconsts.size(), Eq(2));
+    ASSERT_THAT(std::stod(latconsts[0]), DoubleNear(3.208725140430033, 1.e-2));
+    ASSERT_THAT(std::stod(latconsts[1]), DoubleNear(5.239826212595919, 1.e-2));
 
     BEGIN_HIDE_OUTPUT();
     command("clear");
-    command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal");
+    command("kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_006 metal");
 
     command("kim query alpha get_linear_thermal_expansion_coefficient_cubic "
             "crystal=[fcc] species=[Al] units=[1/K] temperature=[293.15] "
             "temperature_units=[K]");
     END_HIDE_OUTPUT();
 
-    ASSERT_THAT(variable->retrieve("alpha"), StrEq("1.656579473023212e-05"));
+    ASSERT_THAT(std::stod(variable->retrieve("alpha")), DoubleNear(1.658279376744496e-05, 1e-7));
 
     BEGIN_HIDE_OUTPUT();
     command("clear");
@@ -645,7 +650,7 @@ TEST_F(KimCommandsTest, kim_query)
     END_HIDE_OUTPUT();
 
     std::string model_list = variable->retrieve("model_list");
-    auto n = model_list.find("EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000");
+    auto n = model_list.find("EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_006");
     ASSERT_TRUE(n != std::string::npos);
 
     BEGIN_HIDE_OUTPUT();