From 32faf17abd78b08489a540249643b1fee7b251d5 Mon Sep 17 00:00:00 2001
From: Dariusz Murakowski <murakdar@mit.edu>
Date: Mon, 6 Jul 2015 12:28:15 -0400
Subject: [PATCH] Add `make` rule for MC code.

---
 Makefile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index e352d7b..3432d77 100644
--- a/Makefile
+++ b/Makefile
@@ -4,6 +4,9 @@ EXECNAME_WF = wf
 
 #SRCS_MC = mc.cpp hamiltonian.cpp population.cpp virus.cpp
 #EXECNAME_MC = mc
+SRCS_MC = mainQEE.cpp io.cpp monteCarlo.cpp qEpitopeEval.cpp tools.cpp
+HEADERS_MC = io.h monteCarlo.h qEpitopeEval.h tools.h dataStructures.h mtrnd.h
+EXECNAME_MC = qee
 
 SRCS_SS = ss.cpp ham_ss.cpp pop_ss.cpp reaction.cpp seqTools.cpp
 EXECNAME_SS = ss
@@ -34,8 +37,8 @@ all: $(EXECNAME_WF) $(EXECNAME_MC) $(EXECNAME_SS)
 $(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_MC): $(SRCS_MC) $(HEADERS_MC) Makefile
+	$(CXX) $(SRCS_MC) -O2 -march=native -o $(EXECNAME_MC)
 
 $(EXECNAME_SS): $(SRCS_SS) $(SRCS_SS:%.cpp=%.h) Makefile
 	$(CXX) $(SRCS_SS) $(CFLAGS) $(LIBDIR) $(INCLUDEDIR) -o $(EXECNAME_SS) $(LIBS)
-- 
2.7.4