delete atomfile style variables with clear command

src/lammps.cpp

@@ -50,6 +50,7 @@
 #include "timer.h"
 #include "universe.h"
 #include "update.h"
+#include "variable.h"
 #include "version.h"
 
 #if defined(LMP_PLUGIN)
@@ -970,6 +971,9 @@ void LAMMPS::destroy()
   delete output;
   output = nullptr;
 
+  // undefine atomfile variables because they use a fix for backing storage
+  input->variable->purge_atomfile();
+
   delete modify;          // modify must come after output, force, update
                           //   since they delete fixes
   modify = nullptr;