ERROR: Did not assign all restart atoms correctly (../read_restart.cpp:521)

please note, that this input fails to run because of undefined
variables and it is not showing how to generate the restart and then
how to read it back to reproduce the failure.
since you are using a rather old intel compiler (there isn't much of a
benefit of that over GNU for C++ anyway unless you are using styles
from USER-INTEL), i'd suggest you try the native GNU compiler for
comparison and possibly also install/compile a newer GNU compiler
suite (8.x?, RHEL/CentOS 6.x ships with very old GNU compilers and is
overall very old) to make certain, you don't have an artifact of the

also, for testing/debugging it would be highly beneficial, if your
input deck was smaller (i.e. fewer atoms in the data file) and less
complex (i.e. less commands in the input script).

it just needs to reliably reproduce the restart problem.