From 1b64003547c3d6237201aa2488649b0687adc5d4 Mon Sep 17 00:00:00 2001
From: fevangelista <francesco.evangelista@emory.edu>
Date: Wed, 1 Jan 2025 18:30:34 -0500
Subject: [PATCH] Final cleanup

---
 forte/sparse_ci/bitarray.hpp                   | 3 ---
 forte/sparse_ci/determinant.hpp                | 2 --
 forte/sparse_ci/sparse_operator_hamiltonian.cc | 1 -
 forte/sparse_ci/sparse_operator_hamiltonian.h  | 4 +++-
 forte/sparse_ci/sq_operator_string.h           | 2 +-
 5 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/forte/sparse_ci/bitarray.hpp b/forte/sparse_ci/bitarray.hpp
index 58bdb0765..93f9ded6b 100644
--- a/forte/sparse_ci/bitarray.hpp
+++ b/forte/sparse_ci/bitarray.hpp
@@ -202,9 +202,6 @@ template <size_t N> class BitArray {
         getword(pos) ^= (-val ^ getword(pos)) & maskbit(pos); // if-free implementation
     }
 
-    void set(size_t pos) { set_bit(pos, true); }
-    void reset(size_t pos) { set_bit(pos, false); }
-
     /// get a word in position pos
     word_t get_word(size_t pos) const { return words_[pos]; }
 
diff --git a/forte/sparse_ci/determinant.hpp b/forte/sparse_ci/determinant.hpp
index 2595f86be..fe0ba5cbb 100644
--- a/forte/sparse_ci/determinant.hpp
+++ b/forte/sparse_ci/determinant.hpp
@@ -76,8 +76,6 @@ template <size_t N> class DeterminantImpl : public BitArray<N> {
     using BitArray<N>::find_first_one;
     using BitArray<N>::find_last_one;
     using BitArray<N>::zero;
-    using BitArray<N>::set;
-    using BitArray<N>::reset;
 
     /// the number of bits divided by two
     static constexpr size_t nbits_half = N / 2;
diff --git a/forte/sparse_ci/sparse_operator_hamiltonian.cc b/forte/sparse_ci/sparse_operator_hamiltonian.cc
index ad6abc766..7cce8e4d9 100644
--- a/forte/sparse_ci/sparse_operator_hamiltonian.cc
+++ b/forte/sparse_ci/sparse_operator_hamiltonian.cc
@@ -40,7 +40,6 @@ SparseOperator sparse_operator_hamiltonian(std::shared_ptr<ActiveSpaceIntegrals>
     size_t nmo = as_ints->nmo();
     H.add_term_from_str("[]", as_ints->nuclear_repulsion_energy() + as_ints->scalar_energy() +
                                   as_ints->frozen_core_energy());
-    Determinant cre, ann;
     for (size_t p = 0; p < nmo; p++) {
         for (size_t q = 0; q < nmo; q++) {
             if (std::fabs(as_ints->oei_a(p, q)) > screen_thresh) {
diff --git a/forte/sparse_ci/sparse_operator_hamiltonian.h b/forte/sparse_ci/sparse_operator_hamiltonian.h
index 366833d8e..072e61e53 100644
--- a/forte/sparse_ci/sparse_operator_hamiltonian.h
+++ b/forte/sparse_ci/sparse_operator_hamiltonian.h
@@ -38,7 +38,9 @@ class ActiveSpaceIntegrals;
 
 /// @brief Generate the a SparseOperator representation of the Hamiltonian using integrals from an
 /// ActiveSpaceIntegrals object
+/// @param as_ints the ActiveSpaceIntegrals object containing the integrals
+/// @param screen_thresh the threshold to screen the integrals
 SparseOperator sparse_operator_hamiltonian(std::shared_ptr<ActiveSpaceIntegrals> as_ints,
-                                           double screen_thresh = 1e-12);
+                                           double screen_thresh = 1e-14);
 
 } // namespace forte
diff --git a/forte/sparse_ci/sq_operator_string.h b/forte/sparse_ci/sq_operator_string.h
index 2a8fff6e4..ce152ce0b 100644
--- a/forte/sparse_ci/sq_operator_string.h
+++ b/forte/sparse_ci/sq_operator_string.h
@@ -90,7 +90,7 @@ class SQOperatorString {
     SQOperatorString();
     /// constructor from a pair of Determinant objects
     SQOperatorString(const Determinant& cre, const Determinant& ann);
-    /// constructor from a pair of Determinant objects
+    /// constructor from initializer lists of creation and annihilation operators
     SQOperatorString(const std::initializer_list<size_t> acre,
                      const std::initializer_list<size_t> bcre,
                      const std::initializer_list<size_t> aann,