From 4de5b1b61240ab531b459249b0c4ca6844b03714 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Fri, 13 Nov 2020 16:30:05 -0700
Subject: [PATCH 1/4] Added README explaining how to run cythonize

---
 src/MLIAPPY/README | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 src/MLIAPPY/README

diff --git a/src/MLIAPPY/README b/src/MLIAPPY/README
new file mode 100644
index 00000000000..12f162da5a1
--- /dev/null
+++ b/src/MLIAPPY/README
@@ -0,0 +1,9 @@
+This package provides a coupling to PyTorch energy models
+via the MLIAP package.
+
+Before compiling LAMMPS with either make or cmake, you have
+to run cythoniz to create the coupling source files
+in the src/MLIAPPY directory e.g.
+
+cd MLIAPPY
+~/anaconda3/bin/cythonize  mliap_model_python_couple.pyx

From 0623817afea8a695772b85d3e3dd8c9540c87d28 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Fri, 20 Nov 2020 11:47:31 -0700
Subject: [PATCH 2/4] Updated README

---
 src/MLIAPPY/README | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/MLIAPPY/README b/src/MLIAPPY/README
index 12f162da5a1..ba15d6eb51d 100644
--- a/src/MLIAPPY/README
+++ b/src/MLIAPPY/README
@@ -2,8 +2,23 @@ This package provides a coupling to PyTorch energy models
 via the MLIAP package.
 
 Before compiling LAMMPS with either make or cmake, you have
-to run cythoniz to create the coupling source files
+to run cythonize to create the coupling source files
 in the src/MLIAPPY directory e.g.
 
 cd MLIAPPY
-~/anaconda3/bin/cythonize  mliap_model_python_couple.pyx
+cythonize mliap_model_python_couple.pyx
+
+When building with make, you will have to add this 
+compiler option, suitably modified for your NumPy:
+
+-I/home/athomps/anaconda3/lib/python3.7/site-packages/numpy/core/include
+
+When bulding with cmake, it should just work, but if you have 
+cmake version older than 3.14, you will have to edit
+this file accordingly:
+more ../../cmake/Modules/Packages/MLIAPPY.cmake
+if(CMAKE_VERSION VERSION_LESS 3.14)
+:
+  target_include_directories(lammps PRIVATE /home/athomps/anaconda3/lib/python3.7/site-packages/numpy/core/include)
+:
+

From 97b77e0f138413162b3d51a6e784ad28517f91eb Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Mon, 30 Nov 2020 19:29:28 -0700
Subject: [PATCH 3/4] Added preprocessor flag

---
 src/MLIAPPY/Install.sh | 53 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100755 src/MLIAPPY/Install.sh

diff --git a/src/MLIAPPY/Install.sh b/src/MLIAPPY/Install.sh
new file mode 100755
index 00000000000..8fccbc2a9c4
--- /dev/null
+++ b/src/MLIAPPY/Install.sh
@@ -0,0 +1,53 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# arg1 = file, arg2 = file it depends on
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+# force rebuild of files using python header
+
+touch ../lmppython.h
+
+# all package files with no dependencies
+
+for file in *.cpp *.h; do
+  test -f ${file} && action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_MLIAPPY |' ../Makefile.package
+  fi
+
+elif (test $1 = 0) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*MLIAPPY[^ \t]* //g' ../Makefile.package
+  fi
+
+fi

From 973382295b1439897e5869ff37cf5ff9915a9c54 Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Thu, 3 Dec 2020 16:47:27 -0700
Subject: [PATCH 4/4] Clean up file

---
 examples/mliappy/in.mliap.pytorch.Ta06A | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/examples/mliappy/in.mliap.pytorch.Ta06A b/examples/mliappy/in.mliap.pytorch.Ta06A
index e44b4352e7b..1d93d6a4249 100644
--- a/examples/mliappy/in.mliap.pytorch.Ta06A
+++ b/examples/mliappy/in.mliap.pytorch.Ta06A
@@ -22,20 +22,6 @@ create_atoms    1 box
 
 mass 1 180.88
 
-python          simple here """
-from __future__ import print_function
-
-def simple():
-  foo = 0
-  print("Inside simple function")
-  try:
-    foo += 1
-  except Exception as e:
-    print("FOO error:", e)
-"""
-
-python          simple invoke
-
 # choose potential
 
 include Ta06A.mliap.pytorch