added in documentation for new heom options, added assertion check to make sure adm_init is of correct length

Author: suarez-va

src/libra_py/dynamics/heom/compute.py

@@ -144,7 +144,6 @@ def transform_adm(rho, rho_scaled, aux_memory, params, direction):
         pack_mtx(aux_memory["rho_unpacked"], rho)
 
 
-#def run_dynamics(dyn_params, Ham, rho_init):
 def run_dynamics(dyn_params, Ham, rho_init, adm_init=None):
     """
     This functions integrates the HEOM for a given system's Hamiltonian, initial conditions, and bath parameters
@@ -278,6 +277,10 @@ def run_dynamics(dyn_params, Ham, rho_init, adm_init=None):
                     The density matrix evolution
                     *_output_level >= 3
 
+                - **auxdenmat** ( CMATRIXList(nn_tot-1, nstates, nstates) )
+                    The auxiliary density matrices excluding the 0th order denmat.
+                    *_output_level >= 4
+
                 [ default: [ "timestep", "time", "denmat" ] ]
 
 
@@ -307,6 +310,10 @@ def run_dynamics(dyn_params, Ham, rho_init, adm_init=None):
             Is the initial density matrix describing the quantum system.
             It's dimensions must be the same as those of the `Ham` variable.
 
+        adm ( CMATRIXList(nn_tot-1, nstates, nstates) )
+            Is the initial auxiliary density matrices describing the quantum system.
+            Does not include the 0th order adm, indexing starts at n=1, should have a length of nn_tot-1.
+            By default the adm's are initialized as 0 matricies.
 
 
     """
@@ -338,7 +345,6 @@ def run_dynamics(dyn_params, Ham, rho_init, adm_init=None):
     comn.check_input(params, default_params, critical_params)
 
     nsteps = params["nsteps"]
-    #nprint = params["nprint"]
     print_freq = int(params["progress_frequency"] * nsteps)
 
     # ============= System ======================
@@ -399,7 +405,7 @@ def run_dynamics(dyn_params, Ham, rho_init, adm_init=None):
         y_ = Py2Cpp_int(list(range(nquant)))
         push_submatrix(rho, rho_init, x_, y_)
     else:
-        # make sure that len(adm_init) == nn_tot-1:
+        assert (len(adm_init) == nn_tot-1), f"adm_init CMATRIXList must be of length nn_tot-1."
         aux_memory["rho_unpacked"][0] = rho_init
         for n in range(1,nn_tot):
             aux_memory["rho_unpacked"][n] = adm_init[n-1]