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

diff --git a/Makefile b/Makefile
index 13ad714..c84f694 100644 (file)
--- 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 (file)
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 (file)
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 (file)
index 0000000..b81f497
--- /dev/null
+++ b/test.st
@@ -0,0 +1,2 @@
+6.000000e-01
+4.000000e-01   0;