# =====================================================================
#  SOC-NAMD-QMMM tutorial deck: formaldehyde in a small water cluster
# =====================================================================
#  QM  : formaldehyde (H2CO), MRSF-TDDFT/BHHLYP/6-31G* on a triplet
#        ROHF reference. Surface hopping runs on the SPIN-ADIABATIC
#        manifold: ns singlets + 3*nt triplet Ms sublevels
#        (= 2 + 3*2 = 8 states), so intersystem crossing (S<->T) is a
#        hop like any other, driven by spin-orbit coupling.
#  MM  : 5 TIP3P waters (OpenMM), coupled to the QM density by ESPF
#        electrostatic embedding.  NoCutoff = isolated (non-periodic).
#
#  This is a MINIMAL demo (nstep=1: one nuclear step). Raise [md] nstep
#  for a real trajectory.  Needs the optional OpenMM backend; the
#  companion files are read relative to this deck.
# ---------------------------------------------------------------------

[input]
# QM geometry (Angstrom): the atoms selected by [qmmm] qm_atoms, in the
# same order.  charge/multiplicity below refer to the QM subsystem.
system=
   6   0.000000   0.000000   0.000000
   8   0.000000   0.000000   1.203000
   1   0.000000   0.943000  -0.589000
   1   0.000000  -0.943000  -0.589000
charge=0
runtype=namd        # nonadiabatic molecular dynamics (surface hopping)
basis=6-31g*
functional=bhhlyp
method=tdhf         # linear-response engine that MRSF is built on
qmmm_flag=True      # turn on QM/MM; configure it in [qmmm] below

[guess]
type=huckel

[scf]
# MRSF-TDDFT starts from a HIGH-SPIN (triplet) ROHF reference.
multiplicity=3
type=rohf

[tdhf]
type=mrsf           # Mixed-Reference Spin-Flip TDDFT
nstate=2            # number of MRSF SINGLET roots to solve (ns)
multiplicity=3      # reference multiplicity (matches [scf])

[properties]
grad=1              # need analytic gradients to propagate nuclei

[md]
nstep=1             # nuclear steps (set to e.g. 200-2000 for real runs)
dt=0.25             # nuclear time step (fs)
active=5            # index of the initially populated spin-adiabatic state
substep=50          # electronic sub-steps per nuclear step (TDC integration)
init_temp=300       # initial temperature (K) for the Maxwell velocities
velocity=maxwell
seed=3              # RNG seed -> reproducible hops
decoherence=edc     # energy-based decoherence correction (Granucci-Persico)
trivial=True        # detect & handle trivial (weakly-avoided) crossings
soc=True            # <-- spin-orbit coupling ON: enables S<->T hops (ISC)
thrshe=0.1          # energy-gap gate (Hartree) guarding spurious S0 hops

[qmmm]
pdb_file=formaldehyde_water.pdb          # full QM+MM coordinates/topology
forcefield_files=formaldehyde.xml tip3p.xml
qm_atoms=0-3                              # which PDB atoms are QM (0-based)
cutoff=NoCutoff                           # isolated cluster (use PME for a box)
embedding=electrostatic                   # full ESPF electrostatic embedding