Add missing multiplication by bmag in GKYL_PROJ_FUNC of gk_species_projection

Makefile

@@ -93,6 +93,15 @@ ifeq (${USE_LUA}, 1)
 	CFLAGS += -DGKYL_HAVE_LUA
 endif
 
+# Read ADAS paths and flags if needed 
+USING_ADAS =
+ADAS_INC_DIR = zero # dummy
+ADAS_LIB_DIR = .
+ifeq (${USE_ADAS}, 1)
+	USING_ADAS = yes
+	CFLAGS += -DGKYL_HAVE_ADAS
+endif
+
 # Build directory
 ifdef USING_NVCC
 	BUILD_DIR ?= cuda-build
@@ -118,8 +127,8 @@ ifeq ($(UNAME), Darwin)
 	SHFLAGS_INSTALL = ${SHFLAGS} -install_name ${PREFIX}/gkylzero/lib/libgkylzero.so
 endif
 
-# Header files
-HEADERS := $(wildcard minus/*.h) $(wildcard zero/*.h) $(wildcard apps/*.h) $(wildcard kernels/*/*.h)
+# Header files 
+HEADERS := $(wildcard minus/*.h) $(wildcard zero/*.h) $(wildcard apps/*.h) $(wildcard kernels/*/*.h) $(wildcard data/adas/*.h)
 # Headers to install
 INSTALL_HEADERS := $(shell ls apps/gkyl_*.h zero/gkyl_*.h | grep -v "priv" | sort)
 INSTALL_HEADERS += $(shell ls minus/*.h)
@@ -128,9 +137,9 @@ INSTALL_HEADERS += $(shell ls minus/*.h)
 INCLUDES = -Iminus -Iminus/STC/include -Izero -Iapps -Iregression -I${BUILD_DIR} ${KERN_INCLUDES} -I${LAPACK_INC} -I${SUPERLU_INC} -I${MPI_INC_DIR} -I${NCCL_INC_DIR} -I${LUA_INC_DIR}
 
 # Directories containing source code
-SRC_DIRS := minus zero apps kernels
+SRC_DIRS := minus zero apps kernels data/adas
 
-# List of regression and unit tests
+# List of regression and unit test
 REGS := $(patsubst %.c,${BUILD_DIR}/%,$(wildcard regression/rt_*.c))
 UNITS := $(patsubst %.c,${BUILD_DIR}/%,$(wildcard unit/ctest_*.c))
 MPI_UNITS := $(patsubst %.c,${BUILD_DIR}/%,$(wildcard unit/mctest_*.c))
@@ -197,6 +206,10 @@ $(BUILD_DIR)/kernels/advection/%.c.o : kernels/advection/%.c
 	$(MKDIR_P) $(dir $@)
 	$(CC) $(CFLAGS) $(NVCC_FLAGS) $(INCLUDES) -c $< -o $@
 
+$(BUILD_DIR)/kernels/bgk/%.c.o : kernels/bgk/%.c
+	$(MKDIR_P) $(dir $@)
+	$(CC) $(CFLAGS) $(NVCC_FLAGS) $(INCLUDES) -c $< -o $@
+
 $(BUILD_DIR)/kernels/bin_op/%.c.o : kernels/bin_op/%.c
 	$(MKDIR_P) $(dir $@)
 	$(CC) $(CFLAGS) $(NVCC_FLAGS) $(INCLUDES) -c $< -o $@
@@ -233,10 +246,6 @@ $(BUILD_DIR)/kernels/maxwell/%.c.o : kernels/maxwell/%.c
 	$(MKDIR_P) $(dir $@)
 	$(CC) $(CFLAGS) $(NVCC_FLAGS) $(INCLUDES) -c $< -o $@
 
-$(BUILD_DIR)/kernels/neutral_react/%.c.o : kernels/neutral_react/%.c
-	$(MKDIR_P) $(dir $@)
-	$(CC) $(CFLAGS) $(NVCC_FLAGS) $(INCLUDES) -c $< -o $@
-
 $(BUILD_DIR)/kernels/pkpm/%.c.o : kernels/pkpm/%.c
 	$(MKDIR_P) $(dir $@)
 	$(CC) $(CFLAGS) $(NVCC_FLAGS) $(INCLUDES) -c $< -o $@
@@ -340,6 +349,7 @@ install: all $(ZERO_SH_INSTALL_LIB) ## Install library and headers
 	${MKDIR_P} ${INSTALL_PREFIX}/gkylzero/lib
 	${MKDIR_P} ${INSTALL_PREFIX}/gkylzero/bin
 	${MKDIR_P} ${INSTALL_PREFIX}/gkylzero/share
+	${MKDIR_P} ${INSTALL_PREFIX}/gkylzero/share/adas
 # Headers
 	cp ${INSTALL_HEADERS} ${INSTALL_PREFIX}/gkylzero/include
 	./minus/gengkylzeroh.sh > ${INSTALL_PREFIX}/gkylzero/include/gkylzero.h

Makefile.sample

@@ -78,6 +78,22 @@ ifeq (${USE_MPI}, 1)
 	CFLAGS += -DGKYL_HAVE_MPI
 endif
 
+# Read NCCL paths and flags if needed (needs MPI and NVCC)
+USING_NCCL =
+NCCL_INC_DIR = zero # dummy
+NCCL_LIB_DIR = .
+ifeq (${USE_NCCL}, 1)
+ifdef USING_MPI
+ifdef USING_NVCC
+	USING_NCCL = yes
+	NCCL_INC_DIR = ${CONF_NCCL_INC_DIR}
+	NCCL_LIB_DIR = ${CONF_NCCL_LIB_DIR}
+	NCCL_LIBS = -lnccl
+	CFLAGS += -DGKYL_HAVE_NCCL
+endif
+endif
+endif
+
 # Read LUA paths and flags if needed 
 USING_LUA =
 LUA_INC_DIR = zero # dummy
@@ -90,9 +106,9 @@ ifeq (${USE_LUA}, 1)
 	CFLAGS += -DGKYL_HAVE_LUA
 endif
 
-INCLUDES = -I${G0_INC_DIR} -I${LAPACK_INC} -I${SUPERLU_INC} -I${MPI_INC_DIR} -I${LUA_INC_DIR}
-LIB_DIRS = -L${LAPACK_LIB_DIR} -L${SUPERLU_LIB_DIR} -L${MPI_LIB_DIR} -L${LUA_LIB_DIR}
-EXT_LIBS = ${LAPACK_LIB} ${SUPERLU_LIB} ${MPI_LIBS} ${LUA_LIBS} -lm -lpthread -ldl
+INCLUDES = -I${G0_INC_DIR} -I${LAPACK_INC} -I${SUPERLU_INC} -I${MPI_INC_DIR} -I${LUA_INC_DIR} -I${NCCL_INC_DIR}
+LIB_DIRS = -L${LAPACK_LIB_DIR} -L${SUPERLU_LIB_DIR} -L${MPI_LIB_DIR} -L${LUA_LIB_DIR} -L${NCCL_LIB_DIR}
+EXT_LIBS = ${LAPACK_LIB} ${SUPERLU_LIB} ${MPI_LIBS} ${LUA_LIBS} ${NCCL_LIBS} -lm -lpthread -ldl
 
 all: rt_twostream
 

README.md

@@ -80,6 +80,10 @@ installed. Likewise, SuperLU **requires you to have cmake** installed.
 in mind that on Apple Macs you do not need to do anything special to use
 LAPACK/BLAS as it comes with the developer tools.
 
+At this step, you can download ADAS data for neutral interactions by adding
+the flag ```--use-adas=yes``` after the other dependencies to be
+installed.
+
 ### Configuring
 
 The (optional) configure step is used when we need to specify the use of