Add LAMMPS build (idaholab#349)

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "contrib/mytrim"]
 	path = contrib/mytrim
 	url = https://github.com/idaholab/mytrim.git
+[submodule "contrib/lammps"]
+	path = contrib/lammps
+	url = https://github.com/dschwen/lammps

contrib/lammps.mk

@@ -0,0 +1,22 @@
+###############################################################################
+################################### LAMMPS ####################################
+###############################################################################
+
+# run Make.sh to recreate the style_*.h files
+OUT := $(shell cd $(LAMMPS_DIR)/src && make yes-GRANULAR && make lmpinstalledpkgs.h && bash ./Make.sh style)
+
+# source files (main stuff and GRANULAR package)
+lammps_cppsrcfiles := $(shell find $(LAMMPS_DIR)/src -maxdepth 1 -name "*.cpp" -not -name "main.cpp")
+
+# We need to be careful about the mpi STUBS (not including those for now)
+#lammps_csrcfiles   := $(shell find $(LAMMPS_DIR) -name "*.c")
+
+app_HEADERS := $(shell find $(LAMMPS_DIR)/src -maxdepth 1 -name "*.h")
+
+# object files
+ADDITIONAL_APP_OBJECTS     += $(patsubst %.cpp, %.$(obj-suffix), $(lammps_cppsrcfiles)) \
+                              $(patsubst %.c, %.$(obj-suffix), $(lammps_csrcfiles))
+
+# dependencies (C, C++ files only)
+ADDITIONAL_APP_DEPS += $(patsubst %.cpp, %.$(obj-suffix).d, $(lammps_cppsrcfiles)) \
+                       $(patsubst %.c, %.$(obj-suffix).d, $(lammps_csrcfiles))

contrib/spparks.mk

@@ -1,5 +1,5 @@
 ###############################################################################
-############################### SPPARKS #######################################
+################################### SPPARKS ###################################
 ###############################################################################
 
 # run Make.sh to recreate the stytle_*.h files
@@ -20,4 +20,3 @@ ADDITIONAL_APP_OBJECTS     += $(patsubst %.cpp, %.$(obj-suffix), $(spparks_cppsr
 # dependencies (C, C++ files only)
 ADDITIONAL_APP_DEPS += $(patsubst %.cpp, %.$(obj-suffix).d, $(spparks_cppsrcfiles)) \
                        $(patsubst %.c, %.$(obj-suffix).d, $(spparks_csrcfiles))
-

doc/content/getting_started/BuildingLAMMPS.md

@@ -0,0 +1,20 @@
+# Building LAMMPS
+
+Check out the LAMMPS repository and use the CMake based build system
+
+```
+git clone [email protected]:lammps/lammps.git
+cd lammps
+mkdir build && cd build
+cmake ../cmake -DBUILD_LIB=yes -DPKG_GRANULAR=yes -DWITH_JPEG=no
+make -j 8
+make install
+```
+
+Adjust the `-j 8` argument to the number of available CPU cores for building.
+
+This builds LAMMPS as a library and installs it (`sudo` may be required on your
+system for the install step). The LAMMPS cmake build system will install a
+pkg-config file `liblammps.pc` (into `/usr/local/lib/pkgconfig/liblammps.pc/` by
+default). Make sure this path is listed in the `PKG_CONFIG_PATH` environment
+variable.

doc/content/getting_started/Installation.md

@@ -15,8 +15,12 @@ or the `MOOSE_DIR` environment variable to point to the MOOSE directory.
 
 ## Install prerequisite packages
 
-Magpie needs GSL (GNU Scientific Library) and the fast Fourier transform library
-FFTW3 installed for a feature complete build. The configuration of these
+The SPPARKS and LAMMPS Monte Carlo and molecular dynamics packages are optional
+dependencies for Magpie. See [building SPPARKS](BuildingSPPARKS.md) and
+[building LAMMPS](BuildingLAMMPS.md) for instructions on how to build them.
+
+Magpie also needs GSL (GNU Scientific Library) and the fast Fourier transform
+library FFTW3 installed for a feature complete build. The configuration of these
 external packages is performed using
 [pkg-config](https://www.freedesktop.org/wiki/Software/pkg-config/).
 Installation of these dependencies is system specific:

magpie.mk

@@ -2,11 +2,20 @@
 # Check the existence of the contrib submodules and build accordingly
 #
 
-SPPARKS_DIR    ?= $(MAGPIE_DIR)/contrib/spparks
-ifneq ($(wildcard $(SPPARKS_DIR)/src/Makefile),)
-  ADDITIONAL_CPPFLAGS += -DSPPARKS_ENABLED
-  app_INCLUDES   += -I $(SPPARKS_DIR)/..
-  include $(MAGPIE_DIR)/contrib/spparks.mk
+# first check if LAMMPS is present
+LAMMPS_DIR    ?= $(MAGPIE_DIR)/contrib/lammps
+ifneq ($(wildcard $(LAMMPS_DIR)/src/Makefile),)
+  ADDITIONAL_CPPFLAGS += -DLAMMPS_ENABLED
+  app_INCLUDES   += -I $(LAMMPS_DIR)/..
+  include $(MAGPIE_DIR)/contrib/lammps.mk
+else
+  # if not check for SPPARKS (we cannot currently build with both enabled!)
+  SPPARKS_DIR    ?= $(MAGPIE_DIR)/contrib/spparks
+  ifneq ($(wildcard $(SPPARKS_DIR)/src/Makefile),)
+    ADDITIONAL_CPPFLAGS += -DSPPARKS_ENABLED
+    app_INCLUDES   += -I $(SPPARKS_DIR)/..
+    include $(MAGPIE_DIR)/contrib/spparks.mk
+  endif
 endif
 
 MYTRIM_DIR    ?= $(MAGPIE_DIR)/contrib/mytrim