MesoHOPS 1.6.1

# MesoHOPS 1.6.1
This commit upgrades MesoHOPS, adding a new trajectory checkpointing system, options for increased HopsStorage efficiency, overhauled initialization of Noise 2, quality-of-life improvements, and various fixes.
### Key improvements and features:
1. **Trajectory Checkpointing**: Checkpointing allows the user to save and load a trajectory as a .npz file with options to alter the noise going forward, greatly simplifying advanced sampling techniques. In a similar vein, the HopsSystem object may now be saved and loaded to hasten initialization.
2. **HopsStorage Step**: HopsStorage may now be set to save data from only selected time points, reducing the RAM costs of storing data. This is distinct from the save_slices method of HopsTrajectory, which conveniently saves the data of HopsStorage to disk and has options for slicing and compressing data to reduce hard disk costs.
3. **Noise2 Input Management**: Noise 2 (typically used for thermal noise and the time-dependent portion of the Hamiltonian) is now initialized with its own parameter dictionary and the user may choose whether to make it purely real. <ins>Noise 2 is no longer automatically multiplied by two and converted to its real portion by the equation-of-motion: scripts that used noise 2 in the past must be updated to account for this!</ins>
4. **Efficient Zero Noise**: When noise model “ZERO” is used, HopsNoise RAM usage no longer scales with system size or simulation time.
5. **DyadicSpectra Static Filter Input Structure**: Updated static filter input structure in DyadicSpectra to properly feed into HopsHierarchy. Checks were added in HopsHierarchy to ensure filters are properly defined for all modes.
6. **Pytest.Raises Standardization**: Unit tests checking for correct error messages no longer use try/except clauses and are now tested using pytest.raises
7. **Spectral Density Streamlining**: <ins>bcf_convert_sdl_to_exp has been deprecated</ins>, and bcf_convert_dl_to_exp_with_Matsubara has been renamed to bcf_convert_dl_to_exp. For treatment of underdamped modes, we recommend using bcf_convert_dl_ud_to_exp.
8. **Version Hash Metadata**: Current git commit hash can now be accessed and saved from HopsStorage, allowing users to store the commit hash at runtime.
9. **HopsDyadic Complex Handling**: Fixed an issue where the _M2_dyad_conversion method was restricting the matrix elements to be real in the case where the provided matrix is a dense array.
These enhancements collectively improve the computational efficiency, maintainability, and convenience of MesoHOPS for current and future applications.

Author: alexiahartzell

pyproject.toml

@@ -6,7 +6,8 @@ dependencies = [
   "scipy",
   "numba",
   "pytest",
-  "pytest-level"
+  "pytest-level",
+  "pytest-cov"
 ]
 requires-python = ">=3.12"
 authors = [

pytest.ini

@@ -1,13 +1,15 @@
-[tool:pytest]
+[pytest]
 testpaths = tests
 python_files = test_*.py
 python_classes = Test*
 python_functions = test_*
+markers =
+    order: enforce execution order of tests
 addopts =
     --verbose
+    --level=1
     --cov=mesohops
     --cov-report=term-missing
     --cov-report=html
     --cov-report=xml
     --cov-fail-under=70
-

src/mesohops/basis/hops_aux.py

@@ -31,7 +31,6 @@ class AuxiliaryVector(Mapping):
         '_index',          # Current index
         '__id_string',     # Unique identifier string
         '__mode_digits',   # Number of digits per mode
-        '__kmax',          # Maximum hierarchy depth
 
         # --- Cached values ---
         '_sum',            # Cached sum of vector elements

src/mesohops/basis/hops_basis.py

@@ -935,7 +935,7 @@ def get_Z2_noise_sparse(self, z_step):
         if self.off_diagonal_couplings:
             # Get the noise associated with system-bath projection operators that
             # couple states in the current basis to a different state.
-            noise_t = (np.conj(z_step[0]) - 2j * np.real(z_step[1]))[
+            noise_t = (np.conj(z_step[0]) - 1j * z_step[1])[
                 self.mode.list_rel_ind_off_diag_L2]
             # Get the noise memory drift associated with system-bath projection
             # operators that couple states in the current basis to a different state.

src/mesohops/basis/hops_fluxfilters.py

@@ -332,6 +332,9 @@ def construct_filter_markov_up(self):
                        filtered out) while False indicates otherwise
                        (positioning is (mode, aux)).
         """
+        if len(self.mode.list_absindex_mode) == 0:
+            return True
+
         M2_mark_filtered_modes = np.array(
             [
                 np.array([param[m] for m in self.mode.list_absindex_mode])
@@ -389,6 +392,9 @@ def construct_filter_triangular_up(self):
                        filtered out) while False indicates otherwise
                        (positioning is (mode, aux)).
         """
+        if len(self.mode.list_absindex_mode) == 0:
+            return True
+
         M2_tri_filtered_modes = np.array(
             [
                 np.array([param[0][m] for m in self.mode.list_absindex_mode])
@@ -442,6 +448,9 @@ def construct_filter_longedge_up(self):
                        filtered out) while False indicates otherwise
                        (positioning is (mode, aux)).
         """
+        if len(self.mode.list_absindex_mode) == 0:
+            return True
+
         M2_le_filtered_modes = np.array(
             [
                 np.array([param[0][m] for m in self.mode.list_absindex_mode])