From 968897e016bfaa2d73514d28eb46e52adc774126 Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Tue, 21 Apr 2015 17:54:36 -0400 Subject: [PATCH] SS-only, with example files. The following command should execute: ./ss -i neutral_4site -s test -ep crossreactive -epT0 20 -e 10 -t 1 -v --- Makefile | 27 +-------------------------- crossreactive.ep | 2 ++ neutral_4site.j | 5 +++++ test.st | 2 ++ 4 files changed, 10 insertions(+), 26 deletions(-) create mode 100644 crossreactive.ep create mode 100644 neutral_4site.j create mode 100644 test.st diff --git a/Makefile b/Makefile index 13ad714..c84f694 100644 --- a/Makefile +++ b/Makefile @@ -1,10 +1,4 @@ -SRCS_WF = wf.cpp hamiltonian.cpp population.cpp virus.cpp -EXECNAME_WF = wf - -SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp -EXECNAME_MC = mc - SRCS_SS = ss.cpp ham_ss.cpp pop_ss.cpp reaction.cpp EXECNAME_SS = ss @@ -24,34 +18,15 @@ else DBGFLAG = -O3 -combine endif -# now the actual build rules, pretty general .PHONY: clean -all: $(EXECNAME_WF) $(EXECNAME_MC) $(EXECNAME_SS) +all: $(EXECNAME_SS) # @echo done making $(EXECNAME) -$(EXECNAME_WF): $(SRCS_WF) $(SRCS_WF:%.cpp=%.h) Makefile - $(CXX) $(SRCS_WF) $(CFLAGS) $(LIBDIR) $(INCLUDEDIR) -o $(EXECNAME_WF) $(LIBS) - -$(EXECNAME_MC): $(SRCS_MC) $(SRCS_MC:%.cpp=%.h) Makefile - $(CXX) $(SRCS_MC) $(CFLAGS) $(LIBDIR) $(INCLUDEDIR) -o $(EXECNAME_MC) $(LIBS) - $(EXECNAME_SS): $(SRCS_SS) $(SRCS_SS:%.cpp=%.h) Makefile $(CXX) $(SRCS_SS) $(CFLAGS) $(LIBDIR) $(INCLUDEDIR) -o $(EXECNAME_SS) $(LIBS) -# concatenate all the source files before compiling -# ./concat.sh $(EXECNAME) $(SRCS) -# $(CXX) -x c++ $(EXECNAME).combined $(CFLAGS) $(LIBDIR) $(INCLUDEDIR) -o $(EXECNAME) $(LIBS) - -# $(CXX) $(SRCS) $(CFLAGS) $(LFLAGS) $(INCLUDES) $(LIBS) -o $(EXECNAME) -# $(CXX) $(CFLAGS) $(INCLUDES) -o $(EXECNAME) $(OBJS) $(LFLAGS) $(LIBS) - -# equivalent way using 'old-fashioned suffix rules' would be .c.o: -#%.o: %.cpp -# $(CXX) -c $(CFLAGS) $(INCLUDES) $< -o $@ - clean: $(RM) *.o $(EXECNAME_WF) $(EXECNAME_MC) $(EXECNAME_SS) -# $(RM) *.o *.combined $(EXECNAME) diff --git a/crossreactive.ep b/crossreactive.ep new file mode 100644 index 0000000..9f594fe --- /dev/null +++ b/crossreactive.ep @@ -0,0 +1,2 @@ +1.0 0 1 | +1.0 | 3 diff --git a/neutral_4site.j b/neutral_4site.j new file mode 100644 index 0000000..970c83b --- /dev/null +++ b/neutral_4site.j @@ -0,0 +1,5 @@ +4 +0 0 : 0.00e+00 1 : 0.00e+00 2 : 0.00e+00 3 : 0.00e+00; +1 1 : 0.00e+00; +2 2 : 0.00e+00 3 : 0.00e+00; +3 3 : 0.00e+00; diff --git a/test.st b/test.st new file mode 100644 index 0000000..b81f497 --- /dev/null +++ b/test.st @@ -0,0 +1,2 @@ +6.000000e-01 +4.000000e-01 0; -- 2.7.4