some changes

README.md

@@ -12,8 +12,11 @@
         <img src="https://readthedocs.org/projects/quantumdna/badge/?version=latest"
             alt="Documentation Status"></a>
     <a href="https://github.com/dehe1011/QuantumDNA/releases">
-        <img src="https://img.shields.io/badge/version-0.1.8-blue"
-            alt="Release"></a>
+        <img src="https://img.shields.io/github/v/release/dehe1011/QuantumDNA"
+            alt="Latest Release"></a>
+    <a href="https://pypi.org/project/qDNA/">
+    <img src="https://img.shields.io/pypi/v/qDNA"
+        alt="PyPI Version"></a>
     <a href='https://coveralls.io/github/dehe1011/QuantumDNA?branch=main'>
         <img src='https://coveralls.io/repos/github/dehe1011/QuantumDNA/badge.svg?branch=main'
             alt='Coverage Status' /></a>
@@ -66,7 +69,7 @@ For a quick installation, you can install the `qDNA` package via pip:
 pip install qDNA
 ```
 
-To ensure compatibility and avoid conflicts with other packages, we recommend using a virtual environment. For detailed installation instructions and alternative methods, please refer to the [Installation Guide](INSTALLATION.md).
+To ensure compatibility and avoid conflicts with other packages, we recommend using a virtual environment. For detailed installation instructions and alternative methods, please refer to the [Installation Guide](installation.md).
 
 ### Example Program
 
@@ -92,7 +95,7 @@ print(f"Average charge separation {dipole} A")
 
 ## Documentation
 
-The documentation for the [latest release](https://quantumdna.readthedocs.io/en/latest/) is available for reading on Read The Docs. Tutorials can be found in a separate GitHub repository [QuantumDNA-notebooks](https://github.com/dehe1011/QuantumDNA-notebooks)
+The documentation for the latest release is available for reading on [Read The Docs](https://quantumdna.readthedocs.io/en/latest/). Tutorials can be found in a separate GitHub repository [QuantumDNA-notebooks](https://github.com/dehe1011/QuantumDNA-notebooks).
 
 ## Graphical User Interface
 

qDNA/__init__.py

@@ -16,4 +16,4 @@
 from .environment import *
 from .dynamics import *
 from .evaluation import *
-from .plotting import *
+from .visualization import *

qDNA/data/raw/config.json

@@ -2,7 +2,7 @@
     "data": {
       "DNA_BASES": ["A", "T", "G", "C", "F"],
       "TB_MODELS": ["WM", "LM", "ELM", "FWM", "FLM", "FELM", "FC"],
-      "SOURCES": ["Hawke2010", "Simserides2014", "Mantela2021", "Simserides2024", "Herb2024", "1BNA"],
+      "SOURCES": ["Hawke2010", "Simserides2014", "Mantela2021", "Simserides2024", "Herb2024", "uni_dimer_seq", "1BNA"],
       "DESCRIPTIONS": ["1P", "2P"],
       "PARTICLES": ["electron", "hole", "exciton"],
       "UNITS": ["meV", "eV", "100meV", "rad/ps", "rad/fs", "1/cm", "K", "J", "1/fs", "1/ps"],

qDNA/data/raw/tb_params/uni_dimer_seq_electron_ELM.json

@@ -0,0 +1 @@
+{"data": {"t_01A02T": -23.11, "h_01A34T": 12.15, "h_02T33A": 12.12, "t_33A34T": -22.53, "E_01A": -4187.49, "E_02T": -4294.38, "E_33A": -4185.61, "E_34T": -4295.99, "r+_01A33A": -4.17, "r-_02T34T": -2.85, "t_02T03T": -7.92, "h_03T32A": -12.16, "t_32A33A": -43.27, "E_03T": -4294.09, "E_32A": -4187.82, "r+_02T32A": 0.73, "r-_03T33A": -5.56, "t_03T04A": 24.11, "h_04A31T": 12.19, "t_31T32A": -23.86, "E_04A": -4188.25, "E_31T": -4293.36, "r+_03T31T": -0.11, "r-_04A32A": 65.12, "t_04A05A": -44.41, "h_05A30T": -12.17, "t_30T31T": -7.15, "E_05A": -4186.87, "E_30T": -4292.1, "r+_04A30T": -0.73, "r-_05A31T": 5.54, "t_05A06G": 38.48, "h_06G29C": 1.27, "t_29C30T": 27.17, "E_06G": -4117.42, "E_29C": -4421.11, "r+_05A29C": -0.02, "r-_06G30T": 4.15, "t_06G07C": 47.55, "h_07C28G": -1.06, "t_28G29C": -31.28, "E_07C": -4419.92, "E_28G": -4115.03, "r+_06G28G": 2.46, "r-_07C29C": -0.91, "t_07C08C": -60.87, "h_08C27G": 1.24, "t_27G28G": 20.09, "E_08C": -4420.76, "E_27G": -4113.86, "r+_07C27G": -0.07, "r-_08C28G": -2.57, "t_08C09G": 29.01, "h_09G26C": -1.15, "t_26C27G": -31.42, "E_09G": -4114.58, "E_26C": -4423.24, "r+_08C26C": 0.03, "r-_09G27G": -30.76, "t_09G10G": 16.68, "h_10G25C": 1.15, "t_25C26C": -59.95, "E_10G": -4116.31, "E_25C": -4421.21, "r+_09G25C": 0.08, "r-_10G26C": 2.56, "t_10G11T": 26.27, "h_11T24A": 12.14, "t_24A25C": -5.01, "E_11T": -4294.27, "E_24A": -4188.18, "r+_10G24A": -3.42, "r-_11T25C": 1.17, "t_11T12C": -20.67, "h_12C23G": 1.29, "t_23G24A": -7.83, "E_12C": -4425.69, "E_23G": -4116.33, "r+_11T23G": -0.59, "r-_12C24A": 0.92, "t_12C13T": -27.39, "h_13T22A": 12.13, "t_22A23G": 39.81, "E_13T": -4295.18, "E_22A": -4185.78, "r+_12C22A": -0.02, "r-_13T23G": -4.45, "t_13T14G": -24.65, "h_14G21C": 1.19, "t_21C22A": -12.17, "E_14G": -4116.29, "E_21C": -4423.77, "r+_13T21C": 0.01, "r-_14G22A": 43.7, "t_14G15A": 6.87, "h_15A20T": 12.13, "t_20T21C": 21.45, "E_15A": -4187.0, "E_20T": -4294.34, "r+_14G20T": 0.64, "r-_15A21C": -0.99, "t_15A16C": -4.5, "h_16C19G": 1.12, "t_19G20T": 26.24, "E_16C": -4428.59, "E_19G": -4116.11, "r+_15A19G": -3.55, "r-_16C20T": 1.16, "t_16C17A": -11.88, "h_17A18T": -12.2, "t_18T19G": 24.46, "E_17A": -4187.71, "E_18T": -4294.32, "r+_16C18T": -0.01, "r-_17A19G": 49.98}, "metadata": {"source": "uni_dimer_seq", "particle": "electron", "tb_model_name": "ELM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/uni_dimer_seq_hole_ELM.json

@@ -0,0 +1 @@
+{"data": {"t_01A02T": 354.8, "h_01A34T": 28.62, "h_02T33A": 28.54, "t_33A34T": 351.84, "E_01A": -8507.82, "E_02T": -9139.1, "E_33A": -8507.05, "E_34T": -9142.61, "r+_01A33A": -20.43, "r-_02T34T": -3.75, "t_02T03T": -82.66, "h_03T32A": -28.6, "t_32A33A": -56.7, "E_03T": -9139.83, "E_32A": -8509.32, "r+_02T32A": 2.55, "r-_03T33A": -29.03, "t_03T04A": -27.37, "h_04A31T": -28.57, "t_31T32A": -26.99, "E_04A": -8509.79, "E_31T": -9140.17, "r+_03T31T": -0.31, "r-_04A32A": -222.88, "t_04A05A": 56.41, "h_05A30T": -28.53, "t_30T31T": -81.36, "E_05A": -8507.77, "E_30T": -9139.32, "r+_04A30T": 2.56, "r-_05A31T": 29.02, "t_05A06G": -12.95, "h_06G29C": 37.81, "t_29C30T": 13.36, "E_06G": -8296.84, "E_29C": -8691.99, "r+_05A29C": -4.89, "r-_06G30T": 7.36, "t_06G07C": 185.05, "h_07C28G": -37.74, "t_28G29C": -177.47, "E_07C": -8691.46, "E_28G": -8295.88, "r+_06G28G": 5.17, "r-_07C29C": -11.05, "t_07C08C": 57.86, "h_08C27G": 37.75, "t_27G28G": 47.75, "E_08C": -8690.26, "E_27G": -8296.48, "r+_07C27G": -2.14, "r-_08C28G": 22.33, "t_08C09G": -18.43, "h_09G26C": -37.84, "t_26C27G": 18.35, "E_09G": -8295.89, "E_26C": -8690.68, "r+_08C26C": -1.03, "r-_09G27G": 24.88, "t_09G10G": 47.59, "h_10G25C": 37.87, "t_25C26C": 58.06, "E_10G": -8297.33, "E_25C": -8692.35, "r+_09G25C": 2.14, "r-_10G26C": -22.18, "t_10G11T": -267.41, "h_11T24A": -28.57, "t_24A25C": 310.22, "E_11T": -9141.51, "E_24A": -8509.07, "r+_10G24A": -8.22, "r-_11T25C": 5.94, "t_11T12C": -26.39, "h_12C23G": 37.74, "t_23G24A": 14.75, "E_12C": -8692.17, "E_23G": -8296.84, "r+_11T23G": -1.13, "r-_12C24A": 62.66, "t_12C13T": -14.37, "h_13T22A": 28.51, "t_22A23G": -12.54, "E_13T": -9142.71, "E_22A": -8508.15, "r+_12C22A": -4.86, "r-_13T23G": -7.42, "t_13T14G": -18.5, "h_14G21C": -37.87, "t_21C22A": 39.16, "E_14G": -8296.31, "E_21C": -8690.4, "r+_13T21C": -0.56, "r-_14G22A": 90.02, "t_14G15A": -14.34, "h_15A20T": -28.57, "t_20T21C": -25.88, "E_15A": -8507.67, "E_20T": -9140.12, "r+_14G20T": 1.14, "r-_15A21C": 62.33, "t_15A16C": -314.15, "h_16C19G": -37.83, "t_19G20T": -266.95, "E_16C": -8691.53, "E_19G": -8296.86, "r+_15A19G": -8.25, "r-_16C20T": -5.95, "t_16C17A": -39.45, "h_17A18T": -28.59, "t_18T19G": -18.12, "E_17A": -8507.22, "E_18T": -9139.51, "r+_16C18T": -0.57, "r-_17A19G": -90.34}, "metadata": {"source": "uni_dimer_seq", "particle": "hole", "tb_model_name": "ELM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/dynamics/solver.py

@@ -148,7 +148,7 @@ def __init__(self, tb_ham, lindblad_diss, **me_kwargs):
         self.init_matrix = self.get_init_matrix()
 
         # set options for the solver
-        self.options = q.Options(method=self.me_kwargs.get("solver_method"))
+        self.options = None
 
         # empty lists to store results
         self.reset()

qDNA/environment/lindblad.py

@@ -21,7 +21,7 @@
 import numpy as np
 import qutip as q
 
-from ..tools import DEFAULTS, UNITS, DNA_BASES, check_diss_kwargs
+from ..tools import DEFAULTS, UNITS, check_diss_kwargs
 from ..utils import get_conversion
 from ..hamiltonian import TB_Ham, add_groundstate
 
@@ -132,11 +132,14 @@ def __init__(self, tb_ham, **diss_kwargs):
         # Relaxation
         self.uniform_relaxation = self.diss_kwargs.get("uniform_relaxation")
         if self.uniform_relaxation:
-            DNA_SITES = DNA_BASES + ["B"]
             relax_rate = self.diss_kwargs["relax_rate"]
-            self.relax_rates = dict(zip(DNA_SITES, [relax_rate] * len(DNA_SITES)))
+            tb_sites = tb_ham.tb_sites_flattened
+            self.relax_rates = dict(zip(tb_sites, [relax_rate] * len(tb_sites)))
         else:
             self.relax_rates = self.diss_kwargs.get("relax_rates")
+            assert set(self.relax_rates.keys()) == set(
+                tb_ham.tb_sites_flattened
+            ), "relax_rates must have the same keys as the tight-binding sites"
 
         # Relaxation operators
         self.relax_ops = self._get_relax_ops()
@@ -229,8 +232,13 @@ def _get_relax_ops(self):
         list
             A list of relaxation operators, each scaled by the square root of the corresponding relaxation rate.
         """
+        if not self.tb_ham.relaxation:
+            return []
 
-        return get_relax_ops(self.relax_rates, self.tb_ham)
+        tb_basis = self.tb_ham.tb_basis
+        tb_basis_sites_dict = self.tb_ham.tb_basis_sites_dict
+
+        return get_relax_ops(tb_basis, tb_basis_sites_dict, self.relax_rates)
 
     def _get_deph_ops(self):
         """

qDNA/environment/relax_ops.py

@@ -28,7 +28,7 @@ def get_relax_op(tb_basis, tb_site):
     return q.Qobj(relax_op)
 
 
-def get_relax_ops(relax_rates, tb_ham):
+def get_relax_ops(tb_basis, tb_basis_sites_dict, relax_rates):
     """
     Generate relaxation operators based on the provided relaxation rates and tight-binding Hamiltonian.
 
@@ -45,10 +45,9 @@ def get_relax_ops(relax_rates, tb_ham):
     """
 
     relax_ops = []
-    if tb_ham.relaxation:
-        for tb_site in tb_ham.tb_basis:
-            relax_rate = relax_rates[tb_ham.tb_basis_sites_dict[tb_site]]
-            if relax_rate != 0:
-                relax_op = get_relax_op(tb_ham.tb_basis, tb_site)
-                relax_ops.append(np.sqrt(relax_rate) * relax_op)
+    for tb_site in tb_basis:
+        relax_rate = relax_rates[tb_basis_sites_dict[tb_site]]
+        if relax_rate != 0:
+            relax_op = get_relax_op(tb_basis, tb_site)
+            relax_ops.append(np.sqrt(relax_rate) * relax_op)
     return relax_ops

qDNA/evaluation/dipole.py

@@ -230,7 +230,7 @@ def calc_dipole_moment_dict(tb_model_name, filename, directory, num_cpu=None):
     save_json(
         dipole_dict,
         kwargs,
-        "dipole_" + filename,
+        "dipole_moment_" + filename,
         directory,
     )
     return dipole_moment_dict

qDNA/evaluation/eq_states.py

@@ -7,6 +7,7 @@
 
 from ..utils import get_conversion
 from ..model import global_to_local, local_to_global
+from ..hamiltonian import delete_groundstate
 
 __all__ = ["get_therm_eq_state", "get_deph_eq_state"]
 
@@ -78,11 +79,16 @@ def get_deph_eq_state(me_solver):
     # Local dephasing
     if me_solver.lindblad_diss.loc_deph_rate:
         # maximally mixed state
-        return np.eye(me_solver.tb_ham.matrix_dim) / me_solver.tb_ham.matrix_dim
+        dim = me_solver.tb_ham.matrix_dim
+        if me_solver.tb_ham.relaxation:
+            dim -= 1
+        return np.eye(dim) / dim
 
     # Global dephasing
     if me_solver.lindblad_diss.glob_deph_rate:
-        loc_init_matrix = me_solver.init_matrix.full()
+        loc_init_matrix = me_solver.init_matrix.full().real
+        if me_solver.tb_ham.relaxation:
+            loc_init_matrix = delete_groundstate(loc_init_matrix)
         _, eigs = me_solver.tb_ham.get_eigensystem()
         glob_init_matrix = local_to_global(loc_init_matrix, eigs)
 

qDNA/gui/plotting_window.py

@@ -2,7 +2,7 @@
 import matplotlib.pyplot as plt
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 
-from ..plotting import plot_pop, plot_pops, plot_coh, plot_fourier
+from ..visualization import plot_pop, plot_pops, plot_coh, plot_fourier
 from ..tools import save_figure
 
 # -----------------------------------------------------------------------------------------------------

qDNA/gui/qdna_app.py

@@ -199,8 +199,3 @@ def enable_plotting_frame(self):
         self.initial_frame.change_state("disabled")
         self.options_frame.change_state("disabled")
         self.plot_options_frame.change_state("normal")
-
-
-if __name__ == "__main__":
-    app = qDNA_app()
-    app.mainloop()

qDNA/hamiltonian/tb_ham.py

@@ -153,6 +153,7 @@ def __init__(self, dna_seq, **ham_kwargs):
             self._relaxation = self.ham_kwargs.get("relaxation")
             self.eh_basis = get_eh_basis(self.tb_model.tb_dims)
             self._nn_cutoff = self.ham_kwargs.get("nn_cutoff")
+
         self.matrix = self.get_matrix()
         self.matrix_dim = self.matrix.shape[0]
         self.backbone = True if self.tb_model.num_strands in (3, 4) else False

qDNA/hamiltonian/tb_matrices.py

@@ -95,8 +95,8 @@ def tb_ham_1P(
             tb_str = f"E_{tb_basis_sites_dict[old_state]}"
         else:
             tb_str = f"{tb_str}_{tb_basis_sites_dict[old_state]}{tb_basis_sites_dict[new_state]}"
-        if tb_str[0] == "h" and tb_str not in tb_param_dict:
-            tb_str = f"{tb_str[0]}_{tb_basis_sites_dict[new_state]}{tb_basis_sites_dict[old_state]}"
+        if tb_str[0] in ["h", "r"] and tb_str not in tb_param_dict:
+            tb_str = f"{tb_str.split('_')[0]}_{tb_basis_sites_dict[new_state]}{tb_basis_sites_dict[old_state]}"
 
         if tb_str not in tb_param_dict:
             raise ValueError(

qDNA/hamiltonian/tb_params.py

@@ -28,14 +28,12 @@ def save_tb_params(
 
     Parameters
     ----------
-    tb_param_dict : dict
+    tb_params : dict
         Dictionary containing the tight-binding parameters.
-    info_dict : dict
+    metadata : dict
         Dictionary with metadata, e.g., `source`, `particle`, and `tb_model_name`.
     directory : str, optional
         Directory to save the file, by default `data/raw/tb_params`.
-    notes : str, optional
-        Additional notes to include in the info_dict, by default None.
 
     Examples
     --------
@@ -58,7 +56,7 @@ def load_tb_params(
 
     Parameters
     ----------
-    info_dict : dict
+    metadata : dict
         Dictionary with metadata, e.g., `source`, `particle`, and `tb_model_name`.
     directory : str, optional
         Directory to load the file from, by default `data/raw/tb_params`.

qDNA/lcao/save_load.py

@@ -77,7 +77,9 @@ def convert_pdb_to_xyz(filepath_pdb):
     elements = []
     coordinates = []
     current_base = None
-    xyz_files = {}
+
+    current_chain = ""
+    current_base_number = 0
 
     # Read the PDB file
     with open(filepath_pdb, "r") as file:
@@ -90,11 +92,26 @@ def convert_pdb_to_xyz(filepath_pdb):
                 z = float(line[46:54].strip())  # Extract Z coordinate
 
                 # Parse base identifier
-                residue_name = line[17:20].strip()
-                residue_sequence_number = line[22:26].strip()
-                base_identifier = (
-                    str(residue_sequence_number).zfill(2) + residue_name[1]
-                )
+                base_identifier = line[17:20].strip()
+                chain_identifier = line[21].strip()
+                base_number = int(line[22:26].strip())
+
+                chain_changes = current_chain != chain_identifier
+                base_changes = current_base_number != base_number
+
+                # checks if the base counter starts from one if the chain changes
+                if chain_changes:
+                    lower_strand = True
+                    num_bases_per_strand = current_base_number
+                    start_from_one = bool(base_number == 1)
+
+                if base_changes and lower_strand and start_from_one:
+                    base_number += num_bases_per_strand
+
+                current_chain = chain_identifier
+                current_base_number = base_number
+
+                base_identifier = str(base_number).zfill(2) + base_identifier[1]
 
                 # If base changes, write the previous base to a new .xyz file
                 if current_base is not None and base_identifier != current_base:

qDNA/lcao/slater_koster.py

@@ -17,8 +17,11 @@ def calc_orbital_overlap(orbital1, orbital2, connection):
 
     vector = np.array(orbital2.coordinates) - np.array(orbital1.coordinates)
     distance = np.linalg.norm(vector)
-    if distance != 0:
-        vector_norm = vector / distance
+
+    if distance == 0:
+        return 0
+
+    vector_norm = vector / distance
 
     orbital_types = [orbital1.orbital_type, orbital2.orbital_type]
 

qDNA/tools/check_input.py

@@ -139,13 +139,6 @@ def check_diss_kwargs(**diss_kwargs):
     assert isinstance(kwargs["relax_rates"], dict), f"relax_rates must be of form dict"
 
     # check values
-    DNA_SITES = CONFIG["DNA_BASES"] + ["B"]
-    assert all(
-        [
-            key in DNA_SITES and isinstance(value, (int, float))
-            for key, value in kwargs["relax_rates"].items()
-        ]
-    )
     assert (
         kwargs["spectral_density"] in CONFIG["SPECTRAL_DENSITIES"]
     ), f"spectral_density must be in {CONFIG['SPECTRAL_DENSITIES']}"

qDNA/plotting/__init__.py → qDNA/visualization/__init__.py

@@ -17,6 +17,7 @@
         "axes.grid": True,  # Always show grid
         "grid.linestyle": "--",  # Grid line style
         "grid.alpha": 0.7,  # Grid transparency
+        "axes.titlesize": 18,  # Font size for title
         "axes.labelsize": 15,  # Font size for axis labels
         "legend.fontsize": 12,  # Font size for legend
         "xtick.labelsize": 12,  # Font size for x-tick labels