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rename from puremd_rc_1003/sPuReMD/src/single_body_interactions.c
rename to sPuReMD/src/single_body_interactions.c
diff --git a/puremd_rc_1003/sPuReMD/src/single_body_interactions.h b/sPuReMD/src/single_body_interactions.h
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/single_body_interactions.h
rename to sPuReMD/src/single_body_interactions.h
diff --git a/puremd_rc_1003/sPuReMD/src/system_props.c b/sPuReMD/src/system_props.c
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/system_props.c
rename to sPuReMD/src/system_props.c
diff --git a/puremd_rc_1003/sPuReMD/src/system_props.h b/sPuReMD/src/system_props.h
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/system_props.h
rename to sPuReMD/src/system_props.h
diff --git a/puremd_rc_1003/sPuReMD/src/testmd.c b/sPuReMD/src/testmd.c
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/testmd.c
rename to sPuReMD/src/testmd.c
diff --git a/puremd_rc_1003/sPuReMD/src/three_body_interactions.c b/sPuReMD/src/three_body_interactions.c
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/three_body_interactions.c
rename to sPuReMD/src/three_body_interactions.c
diff --git a/puremd_rc_1003/sPuReMD/src/three_body_interactions.h b/sPuReMD/src/three_body_interactions.h
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/three_body_interactions.h
rename to sPuReMD/src/three_body_interactions.h
diff --git a/puremd_rc_1003/sPuReMD/src/traj.c b/sPuReMD/src/traj.c
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/traj.c
rename to sPuReMD/src/traj.c
diff --git a/puremd_rc_1003/sPuReMD/src/traj.h b/sPuReMD/src/traj.h
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/traj.h
rename to sPuReMD/src/traj.h
diff --git a/puremd_rc_1003/sPuReMD/src/two_body_interactions.c b/sPuReMD/src/two_body_interactions.c
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/two_body_interactions.c
rename to sPuReMD/src/two_body_interactions.c
diff --git a/puremd_rc_1003/sPuReMD/src/two_body_interactions.h b/sPuReMD/src/two_body_interactions.h
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/two_body_interactions.h
rename to sPuReMD/src/two_body_interactions.h
diff --git a/puremd_rc_1003/sPuReMD/src/vector.c b/sPuReMD/src/vector.c
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/vector.c
rename to sPuReMD/src/vector.c
diff --git a/puremd_rc_1003/sPuReMD/src/vector.h b/sPuReMD/src/vector.h
similarity index 100%
rename from puremd_rc_1003/sPuReMD/src/vector.h
rename to sPuReMD/src/vector.h
diff --git a/puremd_rc_1003/tools/replicate.bash b/tools/replicate.bash
similarity index 100%
rename from puremd_rc_1003/tools/replicate.bash
rename to tools/replicate.bash
diff --git a/puremd_rc_1003/tools/replicate_geo.awk b/tools/replicate_geo.awk
similarity index 100%
rename from puremd_rc_1003/tools/replicate_geo.awk
rename to tools/replicate_geo.awk
diff --git a/puremd_rc_1003/tools/run_sim.py b/tools/run_sim.py
similarity index 97%
rename from puremd_rc_1003/tools/run_sim.py
rename to tools/run_sim.py
index 3c1261a6874db792a22d7b8c25815604a296f8b3..a7be0e2a80ab06ff9538d933b37c29fdb4c3450d 100644
--- a/puremd_rc_1003/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -6,7 +6,7 @@ from subprocess import Popen, PIPE
 from os import environ, path, rename
 from time import time
 
-base_dir = '/mnt/home/ohearnku/PuReMD-dev/puremd_rc_1003'
+base_dir = os.getcwd()
 control_dir = path.join(base_dir, 'environ')
 data_dir = path.join(base_dir, 'data')
 puremd_args = [ \