set stores_ids flag for some fixes as suggested by @sjplimp

src/AMOEBA/fix_amoeba_bitorsion.cpp

@@ -82,6 +82,7 @@ FixAmoebaBiTorsion::FixAmoebaBiTorsion(LAMMPS *lmp, int narg, char **arg) :
   wd_section = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
+  stores_ids = 1;
 
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);

src/AMOEBA/fix_amoeba_pitorsion.cpp

@@ -62,6 +62,7 @@ FixAmoebaPiTorsion::FixAmoebaPiTorsion(LAMMPS *lmp, int narg, char **arg) :
   wd_section = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
+  stores_ids = 1;
 
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);

src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp

@@ -60,6 +60,7 @@ FixSMD_TLSPH_ReferenceConfiguration::FixSMD_TLSPH_ReferenceConfiguration(LAMMPS
   if (atom->map_style == Atom::MAP_NONE)
     error->all(FLERR, "Pair tlsph with partner list requires an atom map, see atom_modify");
 
+  stores_ids = 1;
   maxpartner = 1;
   npartner = nullptr;
   partner = nullptr;

src/MOLECULE/fix_cmap.cpp

@@ -87,6 +87,7 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
   respa_level_support = 1;
   ilevel_respa = 0;
   eflag_caller = 1;
+  stores_ids = 1;
 
   // allocate memory for CMAP data
 

src/PERI/fix_peri_neigh.cpp

@@ -52,6 +52,7 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
   restart_global = 1;
   restart_peratom = 1;
   first = 1;
+  stores_ids = 1;
 
   // perform initial allocation of atom-based arrays
   // register with atom class