MesoHOPS 1.5.0

This commit presents a major upgrade from the previous version of MesoHOPS, with improvements including:
1. Added a HopsDyadic class that inherits from HopsTrajectory and manages spectroscopic simulations in doubled system Hilbert space.
2. Added a DyadicSpectra class as a user-friendly interface for calculating absorption and fluorescence spectra with HopsDyadic. Note that fluorescence is calculated in the impulsive limit (i.e., the incoming field is a short temporal pulse approximated by a delta function) and assuming the population time is longer than the optical dephasing time.
3. Added spectroscopy analysis tools in utils/spectroscopy_analysis.py
4. Updated HopsTrajectory._operator to manage the adaptive basis by including all newly-populated states in the basis and re-activating early-time inchworm integration upon use.
5. Added optional time-windowing to HopsNoise, reducing cache time when accessing large noise arrays.

Author: tarungera18

README.md

@@ -63,7 +63,7 @@ to allow users to run only the tests that take a short time. A properly-written
 
 # Citing MesoHOPS
 When using MesoHOPS version 1.4 or later please cite:
-- B. Citty, J. K. Lynd, T. Gera, L. Varvelo, and D. I. G. B. Raccah, "MesoHops: Size-invariant scaling calculations of multi-excitation open quantum systems," [preprint (2024)](https://arxiv.org/abs/2401.07443). 
+- B. Citty, J. K. Lynd, T. Gera, L. Varvelo, and D. I. G. B. Raccah, "MesoHops: Size-invariant scaling calculations of multi-excitation open quantum systems," [J. Chem. Phys. (2024)](https://doi.org/10.1063/5.0197825). 
 *This paper extends the adaptive algorithm to account for arbitrary couplings between thermal environments and vertical excitation energies. Furthermore, it introduces a low-temperature correction and effective integration of the noise that simplify simulations with ultrafast vibrational relaxations.*
 
 When using the adaptive basis (by setting  $\delta_A,\delta_S>0$) , please also cite:
@@ -75,7 +75,9 @@ When using the linear absorption HOPS equation of motion, please also cite:
 *This paper introduces a new HOPS equation of motion for simulating linear absorption spectra using a pure-state decomposition of the dipole correlation function.*
 
 When using the Dyadic adaptive HOPS (DadHOPS) equations, please also cite:
-- T. Gera, L. Chen, A. Eisfeld, J. R. Reimers, E. J. Taffet, and D. I. G. B. Raccah, "Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach," [J. Chem. Phys. (2023)](https://doi.org/10.1063/5.0141882). 
+- T. Gera, A. Hartzell, L. Chen, A. Eisfeld, and D. I. G. B. Raccah, "Formally exact fluorescence spectroscopy simulations for mesoscale molecular aggregates with $N^0$ scaling," [preprint (2025)](https://arxiv.org/abs/2503.00584).
+*This paper extends the dyadic adaptive Hierarchy of Pure States (DadHOPS) implementation to simulate fluorescence spectra in large aggregates and introduces excitation operator decomposition, a generalization of the previously introduced initial state decomposition. Proof-of-concept calculations show that DadHOPS exhibits size-invariant scaling in large molecular aggregates.*  
+- T. Gera, L. Chen, A. Eisfeld, J. R. Reimers, E. J. Taffet, and D. I. G. B. Raccah, "Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach," [J. Chem. Phys. (2023)](https://doi.org/10.1063/5.0141882).
 *This paper introduces a dyadic adaptive Hierarchy of Pure States (DadHOPS) implementation for simulating linear absorption spectra in large aggregates, as well as an initial state decomposition that allows for convenient scaling. Proof-of-concept calculations show that DadHOPS exhibits size-invariant scaling in large molecular aggregates.*
 
 

mesohops/dynamics/basis_functions.py

@@ -2,7 +2,7 @@
 
 __title__ = "Basis Functions"
 __author__ = "D. I. G. Bennett, B. Citty"
-__version__ = "1.4"
+__version__ = "1.2"
 
 
 def determine_error_thresh(sorted_error, max_error, offset=0.0):

mesohops/dynamics/basis_functions_adaptive.py

@@ -5,7 +5,7 @@
 
 __title__ = "Adaptive Basis Functions"
 __author__ = "D. I. G. Bennett, B. Citty"
-__version__ = "1.4"
+__version__ = "1.2"
 
 
 def error_sflux_hier(Φ, list_s0, n_state, n_hier, H2_sparse_hamiltonian):
@@ -186,7 +186,7 @@ def error_flux_up(Φ, n_state, n_hier, n_hmodes, list_w, K2_aux_bymode,
         E2_error = np.abs(W2_bymode * (1 + K2_aux_bymode)) ** 2
         if F2_filter is not None:
             E2_error *= F2_filter
-        E2_error = np.transpose(M2_mode_from_state.power(2)) @ E2_error
+        E2_error = np.transpose(np.abs(M2_mode_from_state).power(2)) @ E2_error
         E2_error = P2_pop_state * E2_error / hbar ** 2
 
     else:

mesohops/dynamics/bath_corr_functions.py

@@ -3,7 +3,7 @@
 
 __title__ = "bath_corr_functions"
 __author__ = "D. I. G. Bennett, J. K. Lynd"
-__version__ = "1.4"
+__version__ = "1.2"
 
 # Bath Correlation Functions
 # --------------------------