.gitignore

# precompiled python files
*.pyc
*.pyo

# vim and editor leftovers
.*.swp
.*.swo
.*~
*~

# osx leftovers
.DS_Store

# compiled object files and shared/linked libraries
*.o
*.a
*.lo
*.la
*.dll
*.so

# automake-generated files
Makefile.in
cad/Makefile.in
cad/doc/Makefile.in
cad/partlib/Makefile.in
cad/plugins/DNA/Makefile.in
cad/plugins/HDF5_SimResults/Makefile.in
cad/plugins/HDF5_SimResults/src/Makefile.in
cad/plugins/HDF5_SimResults/src/Testing/Makefile.in
cad/plugins/Makefile.in
cad/src/Makefile.in
sim/Makefile.in
sim/src/Makefile.in
acinclude.m4
aclocal.m4
autom4te.cache
config.guess
config.h.in
config.sub
configure
depcomp
install-sh
ltmain.sh
missing

Makefile
cad/Makefile
cad/doc/Makefile
cad/partlib/Makefile
cad/plugins/DNA/Makefile
cad/plugins/HDF5_SimResults/Makefile
cad/plugins/HDF5_SimResults/src/Makefile
cad/plugins/HDF5_SimResults/src/Testing/Makefile
cad/plugins/Makefile
sim/Makefile

config.h
config.h.in~
config.log
config.status
libtool
stamp-h1

.deps
.libs

# these are presently a file in the repo
# but it gets overwritten by automake
cad/src/Makefile
sim/src/Makefile

# other generated files
config.log
cad/plugins/HDF5_SimResults/Makefile
cad/plugins/HDF5_SimResults/config.h
cad/plugins/HDF5_SimResults/config.log
cad/plugins/HDF5_SimResults/config.status
cad/plugins/HDF5_SimResults/libtool
cad/plugins/HDF5_SimResults/src/.deps/
cad/plugins/HDF5_SimResults/src/.libs/
cad/plugins/HDF5_SimResults/src/Makefile
cad/plugins/HDF5_SimResults/src/Testing/.deps/
cad/plugins/HDF5_SimResults/src/Testing/Makefile
cad/plugins/HDF5_SimResults/src/libHDF5_SimResults.la
cad/plugins/HDF5_SimResults/src/libHDF5_SimResults_la-HDF5_SimResults.lo
cad/plugins/HDF5_SimResults/src/libHDF5_SimResults_la-SimResultsDataStore.lo
cad/plugins/HDF5_SimResults/stamp-h1
sim/src/sim.c
sim/src/bends.gen
sim/src/bonds.gen
sim/src/simulator
sim/src/version.h
cad/src/atombase.c
cad/src/samevals.c

*.rej
.*.rej

# run-time generated log
cad/src/ne1log.txt