add USER-CGDNA package with dependencies into the build system

src/.gitignore

@@ -154,6 +154,8 @@
 /bond_morse.h
 /bond_nonlinear.cpp
 /bond_nonlinear.h
+/bond_oxdna_fene.cpp
+/bond_oxdna_fene.h
 /bond_quartic.cpp
 /bond_quartic.h
 /bond_table.cpp
@@ -388,6 +390,10 @@
 /fix_nve_asphere.h
 /fix_nve_asphere_noforce.cpp
 /fix_nve_asphere_noforce.h
+/fix_nve_dot.cpp
+/fix_nve_dot.h
+/fix_nve_dotc_langevin.cpp
+/fix_nve_dotc_langevin.h
 /fix_nh_body.cpp
 /fix_nh_body.h
 /fix_nph_body.cpp
@@ -747,6 +753,9 @@
 /pair_nm_cut_coul_cut.h
 /pair_nm_cut_coul_long.cpp
 /pair_nm_cut_coul_long.h
+/pair_oxdna_*.cpp
+/pair_oxdna_*.h
+/mf_oxdna.h
 /pair_peri_eps.cpp
 /pair_peri_eps.h
 /pair_peri_lps.cpp

src/Depend.sh

@@ -48,6 +48,7 @@ depend () {
 if (test $1 = "ASPHERE") then
   depend GPU
   depend USER-OMP
+  depend USER-CGDNA
   depend USER-INTEL
 fi
 
@@ -96,6 +97,7 @@ if (test $1 = "MOLECULE") then
   depend USER-MISC
   depend USER-OMP
   depend USER-FEP
+  depend USER-CGDNA
   depend USER-INTEL
 fi
 

src/Makefile

@@ -48,7 +48,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  mpiio mscg opt peri poems \
 	  python qeq reax replica rigid shock snap srd voronoi
 
-PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars \
+PACKUSER = user-atc user-awpmd user-cg-cmm user-cgdna user-colvars \
 	   user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
 	   user-intel user-lb user-manifold user-mgpt user-misc user-molfile \
 	   user-nc-dump user-omp user-phonon user-qmmm user-qtb \

src/USER-CGDNA/Install.sh

@@ -0,0 +1,47 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# arg1 = file, arg2 = file it depends on
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+# list of files with dependcies
+
+action  bond_oxdna_fene.cpp bond_fene.h
+action  bond_oxdna_fene.h bond_fene.h
+action  fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
+action  fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
+action  fix_nve_dot.cpp atom_vec_ellipsoid.h
+action  fix_nve_dot.h atom_vec_ellipsoid.h
+action  mf_oxdna.h atom_vec_ellipsoid.h
+action  pair_oxdna_coaxstk.cpp atom_vec_ellipsoid.h
+action  pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
+action  pair_oxdna_excv.cpp atom_vec_ellipsoid.h
+action  pair_oxdna_excv.h atom_vec_ellipsoid.h
+action  pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
+action  pair_oxdna_hbond.h atom_vec_ellipsoid.h
+action  pair_oxdna_stk.cpp atom_vec_ellipsoid.h
+action  pair_oxdna_stk.h atom_vec_ellipsoid.h
+action  pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
+action  pair_oxdna_xstk.h atom_vec_ellipsoid.h