Quantum Chemistry Notebook Documentation (#30)

* Updated documentation content for quantum chemistry notebook about initial state prep and QPE for GSEE

* Added additional information regarding HF, measuring activation energy, and cleaning up the code

* changing name of xyz file from Co4O4 to Co2O9H12

* improved documentation for quantum chemistry notebook

* Updated pylint badge

* added a references section in the quantum chemistry notebook

* pylint fixes for algo_utils

* some pylint fixes for hamiltoniain_utils

* import grouping pylint fixes

* some pylint changes for utils.py

* Updated pylint badge

* Added a sentence to clarify the notebooks computational targets

* reran ap notebook for grabbing re

* made changes to specify how the scaling factor is defined

* reran notebook and assured resource estimates follow standard and makes sense

* Updated pylint badge

* fixed typo for nb

* adding clarified paragraph given feedback

* fixed typos

* rewrote active space comment

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

README.md

@@ -1,4 +1,4 @@
-![pylint](https://img.shields.io/badge/PyLint-9.08-yellow?logo=python&logoColor=white)
+![pylint](https://img.shields.io/badge/PyLint-9.60-yellow?logo=python&logoColor=white)
 # Quantum Computing Application Specifications
 
 Documentation of Applications for Quantum Computers

src/qca/utils/algo_utils.py

@@ -3,20 +3,24 @@
 import random
 import numpy as np
 import networkx as nx
+
 from cirq import Circuit
-from openfermion import count_qubits
 from cirq.contrib import qasm_import
-from pyLIQTR.utils.Hamiltonian import Hamiltonian
+
+from openfermion import count_qubits
 from openfermion.ops.operators import QubitOperator
+from openfermion.circuits import trotter_steps_required, error_bound
+from openfermion.circuits.trotter_exp_to_qgates import trotterize_exp_qubop_to_qasm
+
+from pyLIQTR.utils.Hamiltonian import Hamiltonian
 from pyLIQTR.utils.utils import open_fermion_to_qasm
 from pyLIQTR.circuits.qsp import generate_QSP_circuit
 from pyLIQTR.utils.qsp_helpers import print_to_openqasm
-from openfermion.circuits import trotter_steps_required, error_bound
-from qca.utils.utils import circuit_estimate, estimate_cpt_resources
 from pyLIQTR.gate_decomp.cirq_transforms import clifford_plus_t_direct_transform
-from openfermion.circuits.trotter_exp_to_qgates import trotterize_exp_qubop_to_qasm
 from pyLIQTR.phase_factors.fourier_response.fourier_response import Angler_fourier_response
 
+from qca.utils.utils import circuit_estimate, estimate_cpt_resources
+
 def estimate_qsp(
     pyliqtr_hamiltonian: Hamiltonian,
     evolution_time:float,
@@ -58,7 +62,9 @@ def find_hamiltonian_ordering(of_hamiltonian: QubitOperator) -> list:
     #ordering hamiltonian terms by performing edge coloring to make optimal trotter ordering
     #assuming that any 2 body interactions are ZZ
     sorted_terms = sorted(list(of_hamiltonian.terms.keys()))
-    sorted_terms.sort(key=lambda x: len(x) * 100 + ord(x[0][1])) #Z and X get translated to 90 and 88 respectively, multiplying by 100 ensures interacting term weight is considered
+
+    #Z and X get translated to 90 and 88 respectively, multiplying by 100 ensures interacting term weight is considered
+    sorted_terms.sort(key=lambda x: len(x) * 100 + ord(x[0][1]))
     one_body_terms_ordered = list(filter(lambda x: len(x) == 1, sorted_terms))
     two_body_terms = list(filter(lambda x: len(x) == 2, sorted_terms))
 
@@ -77,7 +83,7 @@ def find_hamiltonian_ordering(of_hamiltonian: QubitOperator) -> list:
         two_body_terms[i] = term
 
     two_body_terms.sort(key=lambda x: x[2])
-    two_body_terms_ordered = list()
+    two_body_terms_ordered = []
     for (i,term) in enumerate(two_body_terms):
         new_item = (term[0],term[1])
         two_body_terms_ordered.append(new_item)

src/qca/utils/hamiltonian_utils.py

@@ -134,7 +134,7 @@ def nx_longitudinal_ising_terms(graph,p,magnitude=1) -> list[tuple[str, float]]:
     n = len(graph.nodes)
     for n1, n2 in graph.edges:
         weight = magnitude if random.random() < p else -magnitude
-        curr_hamil_string = n * 'I' 
+        curr_hamil_string = n * 'I'
         for idx in range(len(graph)):
             if idx == n1 or idx == n2:
                 curr_hamil_string = f'{curr_hamil_string[:idx]}Z{curr_hamil_string[idx+1:]}'
@@ -146,7 +146,7 @@ def nx_transverse_ising_terms(graph: Graph,p,magnitude=0.1) -> list[tuple[str, f
     n = len(graph)
     for idx in range(n):
         w = magnitude if random.random() < p else -magnitude
-        curr_hamil_string = n * 'I' 
+        curr_hamil_string = n * 'I'
         for k in range(n):
             if idx == k:
                 curr_hamil_string = f'{curr_hamil_string[:idx]}X{curr_hamil_string[idx+1:]}'
@@ -161,14 +161,19 @@ def nx_triangle_lattice(lattice_size: int) -> Graph:
             graph.add_edge((i,j),(i+1,j+1))
     return graph
 
-def generate_triangle_hamiltonian(lattice_size: int, longitudinal_weight_prob:float=0.5, transverse_weight_prob:float=1):
+def generate_triangle_hamiltonian(lattice_size: int,
+                                  longitudinal_weight_prob:float=0.5,
+                                  transverse_weight_prob:float=1):
     graph = nx_triangle_lattice(lattice_size)
     graph = flatten_nx_graph(graph)
     H_transverse = nx_transverse_ising_terms(graph, transverse_weight_prob)
     H_longitudinal = nx_longitudinal_ising_terms(graph, longitudinal_weight_prob)
     return H_transverse, H_longitudinal
 
-def generate_square_hamiltonian(lattice_size: int, dim:int, longitudinal_weight_prob:float=0.5, transverse_weight_prob:float=1):
+def generate_square_hamiltonian(lattice_size: int,
+                                dim:int,
+                                longitudinal_weight_prob:float=0.5,
+                                transverse_weight_prob:float=1):
     dimensions = (lattice_size, lattice_size) if dim == 2 else (lattice_size, lattice_size, lattice_size)
     graph = grid_graph(dim=dimensions)
     graph = flatten_nx_graph(graph)
@@ -196,20 +201,20 @@ def assign_hexagon_labels(graph:Graph, x:str='X', y:str='Y', z:str='Z'):
         if r2 - r1 < 0 or c2 - c1 < 0:
             r1, r2 = r2, r1
             c1, c2 = c2, c1
-        
+
         # now that they are ordered correctly, we can assign labels
         label = ''
         if c1 == c2:
             label = z
         # You can differentiate X and Y labels based off nx's node label parity
-        elif (((r1 % 2) + (c1 % 2)) % 2 == 0):
+        elif ((r1 % 2) + (c1 % 2)) % 2 == 0:
             label = y
         else:
             label = x
-        
+
         graph[n1][n2]['label'] = label
 
-def assign_directional_triangular_labels(g:Graph, lattice_size:int) -> None: 
+def assign_directional_triangular_labels(g:Graph, lattice_size:int) -> None:
     for i in range(lattice_size - 1):
         for j in range(lattice_size - 1):
             g[(i,j)][(i+1,j)]['label'] = 'Z'

src/qca/utils/utils.py

@@ -2,11 +2,15 @@
 import re
 import json
 import time
-import pandas as pd
 from statistics import median
+
+import pandas as pd
+
 import matplotlib.pyplot as plt
-from pyLIQTR.utils.utils import count_T_gates
+
 from cirq import Circuit, AbstractCircuit
+
+from pyLIQTR.utils.utils import count_T_gates
 from pyLIQTR.utils.qsp_helpers import circuit_decompose_once, print_to_openqasm
 from pyLIQTR.gate_decomp.cirq_transforms import clifford_plus_t_direct_transform
 
@@ -30,7 +34,7 @@ def get_T_depth_wire(cpt_circuit: AbstractCircuit):
             opstr = str(operator)
             if opstr[0] == 'T':
                 reg_label = opstr[opstr.find("(")+1:opstr.find(")")]
-                if not reg_label in count_dict:
+                if reg_label not in count_dict:
                     count_dict[reg_label] = 1
                 else:
                     count_dict[reg_label] += 1
@@ -87,7 +91,8 @@ def get_T_depth(cpt_circuit: AbstractCircuit):
 def gen_resource_estimate(cpt_circuit: AbstractCircuit,
                           is_extrapolated: bool,
                           total_steps:int = -1,
-                          circ_occurences:int = -1) -> dict:
+                          circ_occurences:int = -1,
+                          bits_precision:int=1) -> dict:
     '''
     Given some clifford + T circuit and a given filename, we grab the logical resource estimates
     from the circuit and then write it to disk. The function also returns the resource dictionary
@@ -115,12 +120,19 @@ def gen_resource_estimate(cpt_circuit: AbstractCircuit,
     }
 
     if total_steps > 0 and is_extrapolated:
-        resource_estimate['t_depth'] = resource_estimate['t_depth'] * total_steps
-        resource_estimate['t_count'] = resource_estimate['t_count'] * total_steps
-        resource_estimate['max_t_depth_wire'] = resource_estimate['max_t_depth_wire'] * total_steps
-        resource_estimate['gate_count'] = resource_estimate['gate_count'] * total_steps
-        resource_estimate['circuit_depth'] = resource_estimate['circuit_depth'] * total_steps
-        resource_estimate['clifford_count'] = resource_estimate['clifford_count'] * total_steps
+        scaling_factor = total_steps
+    elif bits_precision > 0:
+        scaling_factor = pow(2, bits_precision - 1)
+    else:
+        scaling_factor = None
+
+    if scaling_factor:
+        resource_estimate['t_depth'] = resource_estimate['t_depth'] * scaling_factor
+        resource_estimate['t_count'] = resource_estimate['t_count'] * scaling_factor
+        resource_estimate['max_t_depth_wire'] = resource_estimate['max_t_depth_wire'] * scaling_factor
+        resource_estimate['gate_count'] = resource_estimate['gate_count'] * scaling_factor
+        resource_estimate['circuit_depth'] = resource_estimate['circuit_depth'] * scaling_factor
+        resource_estimate['clifford_count'] = resource_estimate['clifford_count'] * scaling_factor
 
     if circ_occurences > 0:
         resource_estimate['subcicruit_occurrences'] = circ_occurences
@@ -168,12 +180,13 @@ def circuit_estimate(
         numsteps: int,
         circuit_name: str,
         algo_name:str,
+        bits_precision:int=1,
         write_circuits:bool = False
     ) -> AbstractCircuit:
     if not os.path.exists(outdir):
         os.makedirs(outdir)
-    
-    subcircuit_counts = dict()
+
+    subcircuit_counts = {}
     for moment in circuit:
         for operation in moment:
             gate_type = type(operation.gate)
@@ -213,7 +226,8 @@ def circuit_estimate(
         subcircuit_name = subcircuit_counts[gate][2]
         resource_estimate = gen_resource_estimate(subcircuit,
                                                   is_extrapolated=False,
-                                                  circ_occurences=subcircuit_counts[gate][0])
+                                                  circ_occurences=subcircuit_counts[gate][0],
+                                                  bits_precision=bits_precision)
         subcircuit_info = {subcircuit_name:resource_estimate}
         subcircuit_re.append(subcircuit_info)
 
@@ -230,6 +244,13 @@ def circuit_estimate(
         total_T_depth_wire += subcircuit_counts[gate][0] * t_depth_wire * numsteps
         total_T_count += subcircuit_counts[gate][0] * t_count * numsteps
         total_clifford_count += subcircuit_counts[gate][0] * clifford_count * numsteps
+
+        # total_gate_count += subcircuit_counts[gate][0] * gate_count * numsteps * pow(2, bits_precision - 1)
+        # total_gate_depth += subcircuit_counts[gate][0] * gate_depth * numsteps * pow(2, bits_precision - 1)
+        # total_T_depth += subcircuit_counts[gate][0] * t_depth * numsteps * pow(2, bits_precision - 1)
+        # total_T_depth_wire += subcircuit_counts[gate][0] * t_depth_wire * numsteps * pow(2, bits_precision - 1)
+        # total_T_count += subcircuit_counts[gate][0] * t_count * numsteps * pow(2, bits_precision - 1)
+        # total_clifford_count += subcircuit_counts[gate][0] * clifford_count * numsteps * pow(2, bits_precision - 1)
 
     outfile_data = f'{outdir}{circuit_name}_high_level.json'
     total_resources = {
@@ -268,4 +289,4 @@ def re_as_json(main_estimate:dict, estimates:list[dict], file_name:str, algo_nam
     with open(file_name, 'w') as f:
             json.dump(main_estimate, f,
                     indent=4,
-                    separators=(',', ': '))
+                    separators=(',', ': '))