Merge branch 'hough'

Author: leios

.gitignore

@@ -0,0 +1,4 @@
+*.o
+gpue
+*.bvox
+*.png

CMakeLists.txt

@@ -0,0 +1,72 @@
+cmake_minimum_required(VERSION 2.8)
+project(gpue_build LANGUAGES CXX CUDA)
+find_package(CUDA QUIET REQUIRED)
+
+set(
+    CUDA_NVCC_FLAGS
+    ${CUDA_NVCC_FLAGS};
+    -O3 -gencode arch=compute_37,code=sm_37 -lcufft -fopenmp
+)
+
+add_executable(
+    gpue
+    src/dynamic.cu
+    include/dynamic.h
+
+    src/ds.cu
+    include/ds.h
+
+    src/edge.cu
+    include/edge.h
+
+    src/evolution.cu
+    include/evolution.h
+
+    src/fileIO.cu
+    include/fileIO.h
+
+    src/kernels.cu
+    include/kernels.h
+
+    src/manip.cu
+    include/manip.h
+
+    src/lattice.cu
+    include/lattice.h
+
+    src/minions.cu
+    include/minions.h
+
+    src/multigpu.cu
+
+    src/node.cu
+    include/node.h
+
+    src/operators.cu
+    include/operators.h
+
+    src/parser.cu
+    include/parser.h
+
+    src/split_op.cu
+    include/split_op.h
+
+    src/tracker.cu
+    include/tracker.h
+
+    src/unit_test.cu
+    include/unit_test.h
+
+    src/vort.cu
+    include/vort.h
+
+    src/vortex_3d.cu
+    include/vortex_3d.h
+
+    src/init.cu
+    include/init.h
+)
+
+target_compile_features(gpue PUBLIC cxx_std_11)
+target_link_libraries(gpue ${CUDA_LIBRARIES} ${CUDA_CUFFT_LIBRARIES})
+set_target_properties(gpue PROPERTIES CUDA_SEPARABLE_COMPILATION ON)

LICENSE LICENSE.txtLICENSE renamed to LICENSE.txt

@@ -1,5 +1,11 @@
-Copyright (c) 2011-2015, Lee J. O'Riordan (mlxd), Tadhg Morgan, Neil 
-Crowley. All rights reserved.
+/***
+GPUE: Split Operator based GPU solver for Nonlinear 
+Schrodinger Equation, Copyright (C) 2011-2017, 
+Lee J. O'Riordan <loriordan@gmail.com>,
+James Schloss <jrs.schloss@gmail.com>,
+Tadhg Morgan, 
+Neil Crowley.
+All rights reserved.
 
 Redistribution and use in source and binary forms, with or without 
 modification, are permitted provided that the following conditions are 
@@ -27,3 +33,5 @@ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
 NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+***/
+

Makefile

@@ -1,80 +1,41 @@
-CUDA_HOME = /apps/free/cuda/7.5.18/
-GPU_ARCH	= sm_30
+CUDA_HOME = /opt/cuda/
+#CUDA_HOME = /apps/free/cuda/7.5.18/
+#CUTT_DIR = cutt/lib
+GPU_ARCH	= sm_50
 OS:=	$(shell uname)
 ifeq ($(OS),Darwin)
 CUDA_LIB	= $(CUDA_HOME)/lib
 CUDA_HEADER	= $(CUDA_HOME)/include
 CC		= $(CUDA_HOME)/bin/nvcc -ccbin /usr/bin/clang --ptxas-options=-v#-save-temps
-CFLAGS		= -g -O3 -m64 -std=c++11
+CFLAGS		= -g -std=c++11 -Wno-deprecated-gpu-targets
 else
 CUDA_LIB	= $(CUDA_HOME)/lib64
 CUDA_HEADER	= $(CUDA_HOME)/include
 CC		= $(CUDA_HOME)/bin/nvcc --ptxas-options=-v --compiler-options -Wall #-save-temps
 CHOSTFLAGS	= #-fopenmp
-CFLAGS		= -g -O3 -std=c++11 -Xcompiler '-std=c++11' -Xcompiler '-fopenmp' #-malign-double
+CFLAGS		= -g -O0 -std=c++11 -Xcompiler '-std=c++11' -Xcompiler '-fopenmp' #-L$(CUTT_DIR) -l:libcutt.a
 endif
 
+CUDA_FLAGS 	= -lcufft
+
 CLINKER		= $(CC) 
 RM		= /bin/rm
 INCFLAGS	= -I$(CUDA_HEADER) 
 LDFLAGS		= -L$(CUDA_LIB) 
 EXECS		= gpue # BINARY NAME HERE
 
-gpue: fileIO.o kernels.o split_op.o tracker.o minions.o ds.o edge.o node.o lattice.o manip.o vort.o
-#node.o edge.o lattice.o
-	$(CC) *.o $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS) -lm -lcufft -lcudart -o gpue
-	#rm -rf ./*.o
-
-split_op.o: ./src/split_op.cu ./include/split_op.h ./include/kernels.h ./include/constants.h ./include/fileIO.h ./include/minions.h Makefile
-	$(CC) -c  ./src/split_op.cu -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) -Xcompiler "-fopenmp" -arch=$(GPU_ARCH)
-
-kernels.o: ./include/split_op.h Makefile ./include/constants.h ./include/kernels.h ./src/kernels.cu
-	$(CC) -c  ./src/kernels.cu -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) -arch=$(GPU_ARCH)
-
-fileIO.o: ./include/fileIO.h ./src/fileIO.cc Makefile
-	$(CC) -c ./src/fileIO.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS)
-
-tracker.o: ./src/tracker.cc ./include/tracker.h ./include/fileIO.h
-	$(CC) -c ./src/tracker.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-minions.o: ./src/minions.cc ./include/minions.h
-	$(CC) -c ./src/minions.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-ds.o: ./src/ds.cc ./include/ds.h
-	$(CC) -c ./src/ds.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-node.o: ./src/node.cc ./include/node.h
-	$(CC) -c ./src/node.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-edge.o: ./src/edge.cc ./include/edge.h
-	$(CC) -c ./src/edge.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-lattice.o: ./src/lattice.cc ./include/lattice.h
-	$(CC) -c ./src/lattice.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-manip.o: ./src/manip.cu ./include/manip.h
-	$(CC) -c ./src/manip.cu -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-vort.o: ./src/vort.cc ./include/vort.h
-	$(CC) -c ./src/vort.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-graphtest.o: ./src/graphtest.cc
-	$(CC) -c ./src/graphtest.cc -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS)
-
-gtest:  edge.o node.o lattice.o graphtest.o
-	$(CC) $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CHOSTFLAGS) edge.o node.o lattice.o graphtest.o -o gtest
+DEPS = ./include/constants.h ./include/ds.h ./include/edge.h ./include/evolution.h ./include/fileIO.h ./include/init.h ./include/kernels.h ./include/lattice.h ./include/manip.h ./include/minions.h ./include/node.h ./include/operators.h ./include/parser.h ./include/split_op.h ./include/tracker.h ./include/unit_test.h ./include/vort.h ./include/vortex_3d.h ./include/dynamic.h
 
-minions: ./src/minions.cc ./include/minions.h minions.o
-	$(CC) minions.o -o mintest $(INCFLAGS) $(CFLAGS) $(LDFLAGS)
+OBJ = fileIO.o kernels.o split_op.o tracker.o minions.o ds.o edge.o node.o lattice.o manip.o vort.o parser.o evolution.o init.o unit_test.o operators.o vortex_3d.o dynamic.o
 
-tracker_test: tracker.o fileIO.o ./src/tracker.cc ./include/fileIO.h ./src/fileIO.cc ./include/tracker.h
-	$(CC) ./tracker.o ./fileIO.o -o tracker_test $(INCFLAGS) $(CFLAGS) $(LDFLAGS)
+%.o: ./src/%.cc $(DEPS)
+	$(CC) -c -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) -Xcompiler "-fopenmp" -arch=$(GPU_ARCH) $<
 
-default:	gpue
-all:		gpue test
+%.o: ./src/%.cu $(DEPS)
+	$(CC) -c -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CUDA_FLAGS) -Xcompiler "-fopenmp" -arch=$(GPU_ARCH) $< -dc
 
-.c.o:
-	$(CC) $(INCFLAGS) $(CFLAGS) -c $<
+gpue: $(OBJ)
+	$(CC) -o $@ $(INCFLAGS) $(CFLAGS) $(LDFLAGS) $(CUDA_FLAGS) -Xcompiler "-fopenmp" -arch=$(GPU_ARCH) $^
 
 clean:
-	@-$(RM) -f r_0 Phi_0 E* px_* py_0* xPy* xpy* ypx* x_* y_* yPx* p0* p1* p2* EKp* EVr* gpot wfc* Tpot 0* V_* K_* Vi_* Ki_* 0i* k s_* si_* *.o *~ PI* $(EXECS) $(OTHER_EXECS) *.dat *.png *.eps *.ii *.i *cudafe* *fatbin* *hash* *module* *ptx test* vort* v_opt*;
+	@-$(RM) -f r_0 Phi_0 E* px_* py_0* xPy* xpy* ypx* x_* y_* yPx* p0* p1* p2* EKp* EVr* gpot wfc* Tpot 0* V_* K_* Vi_* Ki_* 0i* k s_* si_* *.o *~ PI* $(EXECS) $(OTHER_EXECS) *.dat *.eps *.ii *.i *cudafe* *fatbin* *hash* *module* *ptx test* vort* v_opt*;

bin/run_params.conf

@@ -57,11 +57,10 @@
 # -V, -U are the x and y shifts of the kicking potential.
 # -a, turns on the graph calculation code. Necessary for vortex annihilation
 # -K, selects vortex with specified UID for termination. Plot adjacency matrix of initial state to determine which index (graph_0 --- need to do simulation before you get this; will be updated at some point)
-# -D, sets offset for kill vortex distance radially
 
 
 # Sample simulation data sets
--x 256 -y 256 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.65 -o 100 -d 0 -l 1 -s 1 -i 1.0 -P 10000.0 -G 1.0 -L 10 -X 6.28318 -Y 6.28318 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 1 -D 0.0
--x 512 -y 512 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.75 -o 100 -d 1 -l 1 -s 1 -i 1.0 -P 15000.0 -G 1.0 -L 20 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 2 -D 1.0
--x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.85 -o 100 -d 2 -l 1 -s 1 -i 1.0 -P 20000.0 -G 1.0 -L 30 -X 6.28318 -Y 6.28318 -k 0 -O 20.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 3 -D -4.5
--x 2048 -y 2048 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.95 -o 100 -d 3 -l 1 -s 1 -i 1.0 -P 25000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 3.0 -a 0 -K 0 -D 0
+-x 256 -y 256 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.65 -o 100 -d 0 -l 1 -s 1 -i 1.0 -P 10000.0 -G 1.0 -L 10 -X 6.28318 -Y 6.28318 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 1
+-x 512 -y 512 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.75 -o 100 -d 1 -l 1 -s 1 -i 1.0 -P 15000.0 -G 1.0 -L 20 -X 6.28318 -Y 6.28318 -k 0 -O 10.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 2
+-x 1024 -y 1024 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.85 -o 100 -d 2 -l 1 -s 1 -i 1.0 -P 20000.0 -G 1.0 -L 30 -X 6.28318 -Y 6.28318 -k 0 -O 20.0 -W 1 -U 0 -V 0 -S 3.0 -a 1 -K 3
+-x 2048 -y 2048 -T 1e-5 -t 1e-5 -n 1e6 -g 2.01e5 -e 2e5 -p 1000 -r 0 -w 0.95 -o 100 -d 3 -l 1 -s 1 -i 1.0 -P 25000.0 -G 1.0 -L 0 -X 6.28318 -Y 6.28318 -k 0 -O 0.0 -W 1 -U 0 -V 0 -S 3.0 -a 0 -K 0

include/constants.h

@@ -1,36 +1,3 @@
-///@cond LICENSE
-/*** constants.h - GPUE: Split Operator based GPU solver for Nonlinear
-Schrodinger Equation, Copyright (C) 2011-2015, Lee J. O'Riordan
-<loriordan@gmail.com>, Tadhg Morgan, Neil Crowley.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-1. Redistributions of source code must retain the above copyright
-notice, this list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-contributors may be used to endorse or promote products derived from
-this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
 ///@endcond
 //##############################################################################
 /**
@@ -44,7 +11,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *  @section DESCRIPTION
  *  This file maintains macros for physical constants.
  */
- //##############################################################################
+ //#############################################################################
 
 #ifndef CONSTANTS_H
 #define CONSTANTS_H
@@ -53,7 +20,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define HBAR 1.05457148e-34 // m^2 kg/s
 #define MU_N 5.05078324e-27 // J/T  Nuclear magneton
 #define MU_B 9.27400915e-24 // J/T  Bohr magneton
-#define Q 1.602176565e-19 // C  Elementary charge of proton
+//#define Q 1.602176565e-19 // C  Elementary charge of proton
 #define MU_0 4*PI*1e-7 // V*S/A*m or H/m or N/A^2  Vacuum permeability
 #define EPSILON_0 8.854187817620e-12 // F/m  Vacuum permittivity
 #define INV_RT_2 0.7071067811865475 // 1/sqrt(2)