update build system to make it auto-adapt to include python support or not into MLIAP

cmake/CMakeLists.txt

@@ -194,7 +194,6 @@ endif()
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
 pkg_depends(MLIAP SNAP)
-pkg_depends(MLIAP PYTHON)
 pkg_depends(MPIIO MPI)
 pkg_depends(USER-ATC MANYBODY)
 pkg_depends(USER-LB MPI)

cmake/Modules/FindCythonize.cmake

@@ -0,0 +1,30 @@
+# Find the Cythonize tool.
+#
+# This code sets the following variables:
+#
+#  Cythonize_EXECUTABLE
+#
+# adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
+#=============================================================================
+
+if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+else()
+    find_package(Python3 3.6 COMPONENTS Interpreter QUIET)
+endif()
+
+# Use the Cython executable that lives next to the Python executable
+# if it is a local installation.
+if(Python3_EXECUTABLE)
+  get_filename_component(_python_path ${Python3_EXECUTABLE} PATH)
+  find_program(Cythonize_EXECUTABLE
+    NAMES cythonize3 cythonize cythonize.bat
+    HINTS ${_python_path})
+endif()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Cythonize REQUIRED_VARS Cythonize_EXECUTABLE)
+mark_as_advanced(Cythonize_EXECUTABLE)

cmake/Modules/LAMMPSUtils.cmake

@@ -50,6 +50,7 @@ function(check_for_autogen_files source_dir)
     file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
     file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
+    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/MLIAP/mliap_model_python_couple ${source_dir}/MLIAP/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
       get_filename_component(FILENAME "${_SRC}" NAME)
       if(EXISTS ${source_dir}/${FILENAME})

cmake/Modules/Packages/MLIAP.cmake

@@ -1,3 +1,29 @@
-execute_process(COMMAND cythonize mliap_model_python_couple.pyx WORKING_DIRECTORY ../src/MLIAP)
+# if PYTHON package is included we may also include Python support in MLIAP
+set(ENABLE_MLIAP_PYTHON_DEFAULT OFF)
+if(PKG_PYTHON)
+  find_package(Cythonize)
+  if(Cythonize_FOUND)
+    set(ENABLE_MLIAP_PYTHON_DEFAULT ON)
+  endif()
+endif()
 
-target_compile_definitions(lammps PRIVATE -DLMP_MLIAPPY)
+option(ENABLE_MLIAP_PYTHON "Build MLIAP package with Python support" ${ENABLE_MLIAP_PYTHON_DEFAULT})
+
+if(ENABLE_MLIAP_PYTHON)
+  find_package(Cythonize REQUIRED)
+  if(NOT_PKG_PYTHON)
+    message(FATAL_ERROR "Must install PYTHON package for MLIAP_PYTHON")
+  endif()
+
+  set(MLIAP_CYTHON_DIR ${CMAKE_BINARY_DIR}/cython)
+  file(MAKE_DIRECTORY ${MLIAP_CYTHON_DIR})
+  add_custom_command(OUTPUT  ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.cpp ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.h
+            COMMAND            ${CMAKE_COMMAND} -E copy ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.pyx
+            COMMAND            ${Cythonize_EXECUTABLE} ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.pyx -3
+            WORKING_DIRECTORY  ${MLIAP_CYTHON_DIR}
+            MAIN_DEPENDENCY    ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx
+            COMMENT "Generating C++ sources with cythonize...")
+  target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
+  target_sources(lammps PRIVATE ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.cpp)
+  target_include_directories(lammps PRIVATE ${MLIAP_CYTHON_DIR})
+endif()

doc/src/Packages_details.rst

@@ -666,10 +666,10 @@ A general interface for machine-learning interatomic potentials, including PyTor
 
 **Install:**
 
-To use this package, also the :ref:`SNAP package <PKG-SNAP>` 
+To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
-package needs to be installed. If building the *mliappy* model, 
+to be installed.  To make the *mliappy* model available, also the
-use -DLMP_MLIAPPY and the :ref:`PYTHON package <PKG-PYTHON>` 
+:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed and the version of
-package needs to be installed. The version of python must be >3.5.
+python must be 3.5 or later.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
 
@@ -681,8 +681,8 @@ package needs to be installed. The version of python must be >3.5.
 * :doc:`compute_style mliap <compute_mliap>`
 * examples/mliap (see README)
 
-When built with the *mliappy* model using -DLMP_MLIAPPY, this package
+When built with the *mliappy* model this package includes an extension for
-includes an extension for coupling with python models, including PyTorch.
+coupling with python models, including PyTorch.
 In this case, the python interpreter linked to LAMMPS will need cython and numpy installed.
 The examples build models with PyTorch, which would thus need to be installed.
 

lib/python/Makefile.lammps

@@ -2,6 +2,6 @@
 # See the README file for more explanation
 
 python_SYSINC = $(shell which python-config > /dev/null 2>&1 && python-config --includes || :)
-python_SYSLIB = $(shell which python-config > /dev/null 2>&1 && python-config --ldflags || :)
+python_SYSLIB = -lpython3 $(shell which python-config > /dev/null 2>&1 && python-config --ldflags || :)
 python_SYSPATH =
 PYTHON=python

lib/python/Makefile.mliap_python

@@ -0,0 +1,3 @@
+
+../mliap_model_python_couple.cpp: ../mliap_model_python_couple.pyx
+	cythonize -3 ../mliap_model_python_couple.cpp

src/Depend.sh

@@ -106,6 +106,10 @@ if (test $1 = "PERI") then
   depend USER-OMP
 fi
 
+if (test $1 = "PYTHON") then
+  depend MLIAP
+fi
+
 if (test $1 = "RIGID") then
   depend KOKKOS
   depend USER-OMP
@@ -114,6 +118,7 @@ fi
 
 if (test $1 = "SNAP") then
   depend KOKKOS
+  depend MLIAP
 fi
 
 if (test $1 = "USER-CGSDK") then

src/MLIAP/Install.sh

@@ -26,24 +26,42 @@ action () {
   fi
 }
 
+# enforce package dependency
+if (test $1 = 1 || test $1 = 2) then
+  if (test ! -e ../sna.h) then
+     echo "Must install SNAP package to use MLIAP package"
+     exit 1
+  fi
+fi
+
 # all package files with no dependencies
 
-for file in *.cpp *.h; do
+for file in *.cpp *.h *.pyx; do
   test -f ${file} && action $file
 done
 
 # edit 2 Makefile.package files to include/exclude package info
 
 if (test $1 = 1) then
-
+  if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then
     if (test -e ../Makefile.package) then
-    sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_MLIAPPY |' ../Makefile.package
+      sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package
+    fi
+    if (test -e ../Makefile.package.settings) then
+      sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
+      # multiline form needed for BSD sed on Macs
+      sed -i -e '4 i \
+include ..\/..\/lib\/python\/Makefile.mliap_python
+' ../Makefile.package.settings
+    fi
+    cythonize -3 ../mliap_model_python_couple.pyx
   fi
 
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then
-    sed -i -e 's/[^ \t]*-DLMP_MLIAPPY[^ \t]* //g' ../Makefile.package
+    sed -i -e 's/[^ \t]*-DMLIAP_PYTHON[^ \t]* //g' ../Makefile.package
   fi
-
+  rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h
+  sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
 fi

src/MLIAP/compute_mliap.cpp

@@ -21,7 +21,7 @@
 #include "mliap_model_linear.h"
 #include "mliap_model_quadratic.h"
 #include "mliap_descriptor_snap.h"
-#ifdef LMP_MLIAPPY
+#ifdef MLIAP_PYTHON
 #include "mliap_model_python.h"
 #endif
 
@@ -74,12 +74,12 @@ ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) :
         model = new MLIAPModelQuadratic(lmp);
         iarg += 2;
       }
-      #ifdef LMP_MLIAPPY
+#ifdef MLIAP_PYTHON
       else if (strcmp(arg[iarg+1],"mliappy") == 0) {
       model = new MLIAPModelPython(lmp);
       iarg += 2;
       }
-      #endif
+#endif
       else error->all(FLERR,"Illegal compute mliap command");
       modelflag = 1;
     } else if (strcmp(arg[iarg],"descriptor") == 0) {

src/MLIAP/pair_mliap.cpp

@@ -21,7 +21,7 @@
 #include "mliap_model_linear.h"
 #include "mliap_model_quadratic.h"
 #include "mliap_descriptor_snap.h"
-#ifdef LMP_MLIAPPY
+#ifdef MLIAP_PYTHON
 #include "mliap_model_python.h"
 #endif
 
@@ -152,12 +152,12 @@ void PairMLIAP::settings(int narg, char ** arg)
         if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
         model = new MLIAPModelQuadratic(lmp,arg[iarg+2]);
         iarg += 3;
-      #ifdef LMP_MLIAPPY
+#ifdef MLIAP_PYTHON
       } else if (strcmp(arg[iarg+1],"mliappy") == 0) {
           if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
           model = new MLIAPModelPython(lmp,arg[iarg+2]);
           iarg += 3;
-      #endif
+#endif
       } else error->all(FLERR,"Illegal pair_style mliap command");
       modelflag = 1;
     } else if (strcmp(arg[iarg],"descriptor") == 0) {

src/PYTHON/python_impl.cpp

@@ -26,7 +26,7 @@
 #include <cstring>
 #include <Python.h>  // IWYU pragma: export
 
-#ifdef LMP_MLIAPPY
+#ifdef MLIAP_PYTHON
 #include "mliap_model_python.h"
 // The above should somehow really be included in the next file.
 // We could get around this with cython --capi-reexport-cincludes
@@ -59,12 +59,12 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
   // pyMain stores pointer to main module
   external_interpreter = Py_IsInitialized();
 
-  #ifdef LMP_MLIAPPY
+#ifdef MLIAP_PYTHON
   // Inform python intialization scheme of the mliappy module.
   // This -must- happen before python is initialized.
   int err = PyImport_AppendInittab("mliap_model_python_couple", PyInit_mliap_model_python_couple);
   if (err) error->all(FLERR,"Could not register MLIAPPY embedded python module.");
-  #endif
+#endif
 
   Py_Initialize();
   PyEval_InitThreads();

src/Purge.list

@@ -49,6 +49,8 @@ packages_ntopo.h
 # other auto-generated files
 lmpinstalledpkgs.h
 lmpgitversion.h
+mliap_model_python_couple.cpp
+mliap_model_python_couple.h
 # removed on 9 Sep 2020
 mergesort.h
 # renamed on 8 May 2020