From 0d6f9752278e2693c959c8ea6cdd268e4cf23794 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Mon, 26 Feb 2024 19:36:01 -0500
Subject: [PATCH 01/37] add from lattice_vectors, and to and from lenghts and
 angles

---
 freud/data.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/freud/data.py b/freud/data.py
index 87c0c0bfb..978958f55 100644
--- a/freud/data.py
+++ b/freud/data.py
@@ -233,6 +233,21 @@ def hex(cls):
         fractions = np.array([[0, 0, 0], [0.5, 0.5, 0]])
         return cls([1, np.sqrt(3)], fractions)
 
+    @classmethod
+    def from_lattice_vectors(cls, lattice_vectors, unique_positions):
+        """Create a unit cell from lattice vectors.
+
+        Args:
+            lattice_vectors (:math:`(3, 3)` :class:`np.ndarray
+                The lattice vectors. Lattice vector a1 is lattice_vectors[:, 0], etc.
+            unique_positions (:math:`(N_{points}, 3)` :class:`np.ndarray`):
+                The basis positions.
+
+        Returns:
+            :class:`~.UnitCell`: A unit cell with the given lattice vectors.
+        """
+        return cls(freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions)
+
 
 def make_random_system(box_size, num_points, is2D=False, seed=None):
     r"""Helper function to make random points with a cubic or square box.

From 0717da15a9725ad513c0444d877e12fa07f98c43 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Mon, 26 Feb 2024 19:36:22 -0500
Subject: [PATCH 02/37] Add methods to convert box dimensions and angles

---
 freud/box.pyx | 70 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)

diff --git a/freud/box.pyx b/freud/box.pyx
index e6203fa26..395420045 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -689,6 +689,17 @@ cdef class Box:
                            [0, self.Ly, self.yz * self.Lz],
                            [0, 0, self.Lz]])
 
+    def to_box_lengths_and_angles(self):
+        r"""Return the box lengths and angles.
+
+        Returns:
+            tuple: The box lengths and angles in radians
+        """
+        alpha = np.arccos((self.xy*self.xz+self.yz)/(np.sqrt(1+self.xy**2)*np.sqrt(1+self.xz**2+self.yz**2)))
+        beta = np.arccos(self.xz/np.sqrt(1+self.xz**2+self.yz**2))
+        gamma = np.arccos(self.xy/np.sqrt(1+self.xy**2))
+        return (self.Lx, self.Ly, self.Lz, alpha, beta, gamma)
+
     def __repr__(self):
         return ("freud.box.{cls}(Lx={Lx}, Ly={Ly}, Lz={Lz}, "
                 "xy={xy}, xz={xz}, yz={yz}, "
@@ -921,6 +932,65 @@ cdef class Box:
                             "positional argument: L")
         return cls(Lx=L, Ly=L, Lz=0, xy=0, xz=0, yz=0, is2D=True)
 
+    @classmethod
+    def from_lattice_vectors(cls, lattice_vectors, dimensions=None):
+        """Create a unit cell from lattice vectors.
+
+        Args:
+            lattice_vectors (:math:`(3, 3)` :class:`np.ndarray
+                The lattice vectors. Lattice vector a1 is lattice_vectors[:, 0], etc.
+            dimensions (int): The number of dimensions (Default value = :code:`None`)
+
+        Returns:
+            :class:`~.UnitCell`: A unit cell with the given lattice vectors.
+        """
+        lattice_matrix = np.asarray(lattice_vectors, dtype=np.float32)
+        v0 = lattice_matrix[:, 0]
+        v1 = lattice_matrix[:, 1]
+        v2 = lattice_matrix[:, 2]
+        Lx = np.sqrt(np.dot(v0, v0))
+        a2x = np.dot(v0, v1) / Lx
+        Ly = np.sqrt(np.dot(v1, v1) - a2x * a2x)
+        xy = a2x / Ly
+        v0xv1 = np.cross(v0, v1)
+        v0xv1mag = np.sqrt(np.dot(v0xv1, v0xv1))
+        Lz = np.dot(v2, v0xv1) / v0xv1mag
+        if Lz != 0:
+            a3x = np.dot(v0, v2) / Lx
+            xz = a3x / Lz
+            yz = (np.dot(v1, v2) - a2x * a3x) / (Ly * Lz)
+        else:
+            xz = yz = 0
+        if dimensions is None:
+            dimensions = 2 if Lz == 0 else 3
+        return cls.from_box([Lx, Ly, Lz, xy, xz, yz], dimensions=dimensions)
+
+    @classmethod
+    def from_box_lengths_and_angles(cls, Lx, Ly, Lz, alpha, beta, gamma, dimensions=None):
+        r"""Construct a box from lengths and angles.
+
+        Args:
+            Lx (float): The length in the x direction
+            Ly (float): The length in the y direction
+            Lz (float): The length in the z direction
+            alpha (float): The angle between the y and z axes in radians
+            beta (float): The angle between the x and z axes in radians
+            gamma (float): The angle between the x and y axes in radians
+            dimensions (int): The number of dimensions (Default value = :code:`None`)
+
+        Returns:
+            :class:`freud.box.Box`: The resulting box object.
+        """
+        a1 = np.array([Lx, 0, 0])
+        a2 = np.array([Ly * np.cos(gamma), Ly * np.sin(gamma), 0])
+        a3x = np.cos(beta)
+        a3y = (np.cos(alpha) - np.cos(beta) * np.cos(gamma)) / np.sin(gamma)
+        a3z = np.sqrt(1 - a3x**2 - a3y**2)
+        a3 = np.array([Lz * a3x, Lz * a3y, Lz * a3z])
+        if dimensions is None:
+            dimensions = 2 if Lz == 0 else 3
+        return cls.from_lattice_vectors(np.array([a1, a2, a3]).T, dimensions=dimensions)
+
 
 cdef BoxFromCPP(const freud._box.Box & cppbox):
     b = Box(cppbox.getLx(), cppbox.getLy(), cppbox.getLz(),

From 5a388bf922ccfc666036b2f7cc65dffbf679a2a0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 7 Mar 2024 17:22:37 +0000
Subject: [PATCH 03/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 freud/data.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/freud/data.py b/freud/data.py
index 978958f55..4e39414f5 100644
--- a/freud/data.py
+++ b/freud/data.py
@@ -246,7 +246,9 @@ def from_lattice_vectors(cls, lattice_vectors, unique_positions):
         Returns:
             :class:`~.UnitCell`: A unit cell with the given lattice vectors.
         """
-        return cls(freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions)
+        return cls(
+            freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions
+        )
 
 
 def make_random_system(box_size, num_points, is2D=False, seed=None):

From 58a56f63237da9b6add42f7cc93f04a57159e4ce Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 11:56:09 +0100
Subject: [PATCH 04/37] add type hints and a class method from box lengths and
 angles for unit cell class

---
 freud/data.py | 39 +++++++++++++++++++++++++++++++++++++--
 1 file changed, 37 insertions(+), 2 deletions(-)

diff --git a/freud/data.py b/freud/data.py
index 978958f55..98624d34d 100644
--- a/freud/data.py
+++ b/freud/data.py
@@ -234,7 +234,9 @@ def hex(cls):
         return cls([1, np.sqrt(3)], fractions)
 
     @classmethod
-    def from_lattice_vectors(cls, lattice_vectors, unique_positions):
+    def from_lattice_vectors(
+        cls, lattice_vectors: np.ndarray, unique_positions: np.ndarray
+    ):
         """Create a unit cell from lattice vectors.
 
         Args:
@@ -246,7 +248,40 @@ def from_lattice_vectors(cls, lattice_vectors, unique_positions):
         Returns:
             :class:`~.UnitCell`: A unit cell with the given lattice vectors.
         """
-        return cls(freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions)
+        return cls(
+            freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions
+        )
+
+    @classmethod
+    def from_box_lengths_and_angles(
+        cls,
+        Lx: float,
+        Ly: float,
+        Lz: float,
+        alpha: float,
+        beta: float,
+        gamma: float,
+        unique_positions: np.ndarray,
+    ):
+        """Create a unit cell from box lengths and angles.
+
+        Args:
+            Lx (float): The length of the box in the x direction.
+            Ly (float): The length of the box in the y direction.
+            Lz (float): The length of the box in the z direction.
+            alpha (float): The angle between the x and y lattice vectors.
+            beta (float): The angle between the x and z lattice vectors.
+            gamma (float): The angle between the y and z lattice vectors.
+            unique_positions (:math:`(N_{points}, 3)` :class:`np.ndarray
+                The basis positions.
+
+        Returns:
+            :class:`~.UnitCell`: A unit cell with the given box lengths and angles.
+        """
+        return cls(
+            freud.box.Box.from_box_lengths_and_angles(Lx, Ly, Lz, alpha, beta, gamma),
+            unique_positions,
+        )
 
 
 def make_random_system(box_size, num_points, is2D=False, seed=None):

From 746b923269152c1b7892dcca1b7d254855c2b993 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 11:56:18 +0100
Subject: [PATCH 05/37] add type hints

---
 freud/box.pyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 395420045..0662b9a5e 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -933,7 +933,7 @@ cdef class Box:
         return cls(Lx=L, Ly=L, Lz=0, xy=0, xz=0, yz=0, is2D=True)
 
     @classmethod
-    def from_lattice_vectors(cls, lattice_vectors, dimensions=None):
+    def from_lattice_vectors(cls, lattice_vectors:np.ndarray, dimensions:int=None):
         """Create a unit cell from lattice vectors.
 
         Args:
@@ -966,7 +966,7 @@ cdef class Box:
         return cls.from_box([Lx, Ly, Lz, xy, xz, yz], dimensions=dimensions)
 
     @classmethod
-    def from_box_lengths_and_angles(cls, Lx, Ly, Lz, alpha, beta, gamma, dimensions=None):
+    def from_box_lengths_and_angles(cls, Lx:float, Ly:float, Lz:float, alpha:float, beta:float, gamma:float, dimensions:int=None):
         r"""Construct a box from lengths and angles.
 
         Args:

From c7ad750988fae1864af29d88d36673d22ba5c567 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 20 Mar 2024 11:04:52 +0000
Subject: [PATCH 06/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 freud/data.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/freud/data.py b/freud/data.py
index 3d249e25a..98624d34d 100644
--- a/freud/data.py
+++ b/freud/data.py
@@ -249,9 +249,7 @@ def from_lattice_vectors(
             :class:`~.UnitCell`: A unit cell with the given lattice vectors.
         """
         return cls(
-            
             freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions
-        
         )
 
     @classmethod

From c399ff32bc47a688ba037f285e8ed34df6f26bfb Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 13:01:42 +0100
Subject: [PATCH 07/37] fix format

---
 freud/box.pyx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 0662b9a5e..85f8c7400 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -933,7 +933,7 @@ cdef class Box:
         return cls(Lx=L, Ly=L, Lz=0, xy=0, xz=0, yz=0, is2D=True)
 
     @classmethod
-    def from_lattice_vectors(cls, lattice_vectors:np.ndarray, dimensions:int=None):
+    def from_lattice_vectors(cls, lattice_vectors: np.ndarray, dimensions: int = None):
         """Create a unit cell from lattice vectors.
 
         Args:
@@ -966,7 +966,8 @@ cdef class Box:
         return cls.from_box([Lx, Ly, Lz, xy, xz, yz], dimensions=dimensions)
 
     @classmethod
-    def from_box_lengths_and_angles(cls, Lx:float, Ly:float, Lz:float, alpha:float, beta:float, gamma:float, dimensions:int=None):
+    def from_box_lengths_and_angles(cls, Lx: float, Ly: float, Lz: float, alpha: float,
+    beta: float, gamma: float, dimensions: int = None):
         r"""Construct a box from lengths and angles.
 
         Args:

From 2a995326841ae01638f499f613d5e6473e3d91e8 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 13:09:49 +0100
Subject: [PATCH 08/37] more formatting fixes

---
 freud/box.pyx | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 85f8c7400..34e63997e 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -695,7 +695,10 @@ cdef class Box:
         Returns:
             tuple: The box lengths and angles in radians
         """
-        alpha = np.arccos((self.xy*self.xz+self.yz)/(np.sqrt(1+self.xy**2)*np.sqrt(1+self.xz**2+self.yz**2)))
+        alpha = np.arccos(
+            (self.xy * self.xz + self.yz)
+            / (np.sqrt(1 + self.xy**2) * np.sqrt(1 + self.xz**2 + self.yz**2))
+        )
         beta = np.arccos(self.xz/np.sqrt(1+self.xz**2+self.yz**2))
         gamma = np.arccos(self.xy/np.sqrt(1+self.xy**2))
         return (self.Lx, self.Ly, self.Lz, alpha, beta, gamma)
@@ -966,8 +969,16 @@ cdef class Box:
         return cls.from_box([Lx, Ly, Lz, xy, xz, yz], dimensions=dimensions)
 
     @classmethod
-    def from_box_lengths_and_angles(cls, Lx: float, Ly: float, Lz: float, alpha: float,
-    beta: float, gamma: float, dimensions: int = None):
+    def from_box_lengths_and_angles(
+        cls,
+        Lx: float,
+        Ly: float,
+        Lz: float,
+        alpha: float,
+        beta: float,
+        gamma: float,
+        dimensions: int = None,
+    ):
         r"""Construct a box from lengths and angles.
 
         Args:

From 16d028a94fc5d257d36eadffe82d49a0ef9adc00 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 14:29:59 +0100
Subject: [PATCH 09/37] fixes to logic and docs to all new functions

---
 freud/box.pyx | 44 +++++++++++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 19 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 34e63997e..4d8c0a8a9 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -693,7 +693,7 @@ cdef class Box:
         r"""Return the box lengths and angles.
 
         Returns:
-            tuple: The box lengths and angles in radians
+            tuple: The box vector lengths and angles in radians
         """
         alpha = np.arccos(
             (self.xy * self.xz + self.yz)
@@ -701,7 +701,12 @@ cdef class Box:
         )
         beta = np.arccos(self.xz/np.sqrt(1+self.xz**2+self.yz**2))
         gamma = np.arccos(self.xy/np.sqrt(1+self.xy**2))
-        return (self.Lx, self.Ly, self.Lz, alpha, beta, gamma)
+        L1 = self.Lx
+        a2 = [self.Ly*self.xy, self.Ly,0] 
+        a3 = [self.Lz*self.xz, self.Lz*self.yz, self.Lz]
+        L2 = np.linalg.norm(a2)
+        L3 = np.linalg.norm(a3)
+        return (L1, L2, L3, alpha, beta, gamma)
 
     def __repr__(self):
         return ("freud.box.{cls}(Lx={Lx}, Ly={Ly}, Lz={Lz}, "
@@ -936,21 +941,22 @@ cdef class Box:
         return cls(Lx=L, Ly=L, Lz=0, xy=0, xz=0, yz=0, is2D=True)
 
     @classmethod
-    def from_lattice_vectors(cls, lattice_vectors: np.ndarray, dimensions: int = None):
+    def from_lattice_vectors(cls, lattice_vectors, dimensions: int = None):
         """Create a unit cell from lattice vectors.
 
         Args:
-            lattice_vectors (:math:`(3, 3)` :class:`np.ndarray
-                The lattice vectors. Lattice vector a1 is lattice_vectors[:, 0], etc.
+            lattice_vectors (array-like):
+                The lattice vectors. The dimensions of the object should be 3x3. Lattice
+                vector a1 is lattice_vectors[:, 0], etc. 
             dimensions (int): The number of dimensions (Default value = :code:`None`)
 
         Returns:
             :class:`~.UnitCell`: A unit cell with the given lattice vectors.
         """
         lattice_matrix = np.asarray(lattice_vectors, dtype=np.float32)
-        v0 = lattice_matrix[:, 0]
-        v1 = lattice_matrix[:, 1]
-        v2 = lattice_matrix[:, 2]
+        v0 = lattice_matrix[0]
+        v1 = lattice_matrix[1]
+        v2 = lattice_matrix[2]
         Lx = np.sqrt(np.dot(v0, v0))
         a2x = np.dot(v0, v1) / Lx
         Ly = np.sqrt(np.dot(v1, v1) - a2x * a2x)
@@ -971,9 +977,9 @@ cdef class Box:
     @classmethod
     def from_box_lengths_and_angles(
         cls,
-        Lx: float,
-        Ly: float,
-        Lz: float,
+        L1: float,
+        L2: float,
+        L3: float,
         alpha: float,
         beta: float,
         gamma: float,
@@ -982,9 +988,9 @@ cdef class Box:
         r"""Construct a box from lengths and angles.
 
         Args:
-            Lx (float): The length in the x direction
-            Ly (float): The length in the y direction
-            Lz (float): The length in the z direction
+            L1 (float): The length of the first lattice vector
+            L2 (float): The length of the second lattice vector
+            L3 (float): The length of the third lattice vector
             alpha (float): The angle between the y and z axes in radians
             beta (float): The angle between the x and z axes in radians
             gamma (float): The angle between the x and y axes in radians
@@ -993,15 +999,15 @@ cdef class Box:
         Returns:
             :class:`freud.box.Box`: The resulting box object.
         """
-        a1 = np.array([Lx, 0, 0])
-        a2 = np.array([Ly * np.cos(gamma), Ly * np.sin(gamma), 0])
+        a1 = np.array([L1, 0, 0])
+        a2 = np.array([L2 * np.cos(gamma), L2 * np.sin(gamma), 0])
         a3x = np.cos(beta)
         a3y = (np.cos(alpha) - np.cos(beta) * np.cos(gamma)) / np.sin(gamma)
         a3z = np.sqrt(1 - a3x**2 - a3y**2)
-        a3 = np.array([Lz * a3x, Lz * a3y, Lz * a3z])
+        a3 = np.array([L3 * a3x, L3 * a3y, L3 * a3z])
         if dimensions is None:
-            dimensions = 2 if Lz == 0 else 3
-        return cls.from_lattice_vectors(np.array([a1, a2, a3]).T, dimensions=dimensions)
+            dimensions = 2 if L3 == 0 else 3
+        return cls.from_lattice_vectors(np.array([a1, a2, a3]), dimensions=dimensions)
 
 
 cdef BoxFromCPP(const freud._box.Box & cppbox):

From dc74488edffca77898d46001d433677dcc73e4c7 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 14:30:09 +0100
Subject: [PATCH 10/37] add tests

---
 tests/test_box_Box.py | 57 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index 1b6daff5e..a613ffdf1 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -485,6 +485,63 @@ def test_from_box(self):
         box7 = freud.box.Box.from_matrix(box.to_matrix())
         assert np.isclose(box.to_matrix(), box7.to_matrix()).all()
 
+    def test_standard_orthogonal_box(self):
+        box = freud.box.Box.from_box((1, 2, 3, 0, 0, 0))
+        Lx, Ly, Lz, alpha, beta, gamma = box.to_box_lengths_and_angles()
+        npt.assert_allclose(
+            (Lx, Ly, Lz, alpha, beta, gamma), (1, 2, 3, np.pi / 2, np.pi / 2, np.pi / 2)
+        )
+
+    def test_to_and_from_box_lengths_and_angles(self):
+        original_box_lengths_and_angles = (
+            1,
+            2,
+            3,
+            np.pi / 3,
+            np.pi / 2.25,
+            np.pi / 2.35,
+        )
+        box = freud.box.Box.from_box_lengths_and_angles(
+            *original_box_lengths_and_angles
+        )
+        lengths_and_angles_computed = box.to_box_lengths_and_angles()
+        assert np.allclose(lengths_and_angles_computed, original_box_lengths_and_angles)
+
+    def test_from_lattice_vectors_cubic_lattice(self):
+        lattice_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
+        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors)
+        assert unit_cell.Lx == 1
+        assert unit_cell.Ly == 1
+        assert unit_cell.Lz == 1
+        assert unit_cell.xy == 0
+        assert unit_cell.xz == 0
+        assert unit_cell.yz == 0
+
+    def test_from_lattice_vectors_non_cubic_lattice(self):
+        box = freud.box.Box.from_lattice_vectors([[1, 0, 0], [0, 2, 0], [0, 0, 3]])
+        assert box.Lx == 1
+        assert box.Ly == 2
+        assert box.Lz == 3
+        assert box.xy == 0
+        assert box.xz == 0
+        assert box.yz == 0
+
+    def test_tilted_lattice(self):
+        lattice_vectors = np.array([[1, 0, 0], [0.5, np.sqrt(3) / 2, 0], [0, 0, 1]])
+        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors)
+        assert np.isclose(unit_cell.Lx, 1.0)
+        assert np.isclose(unit_cell.Ly, np.sqrt(3) / 2)
+        assert np.isclose(unit_cell.Lz, 1.0)
+        assert np.isclose(unit_cell.xy, np.sqrt(3) / 3)
+        assert np.isclose(unit_cell.xz, 0.0)
+        assert np.isclose(unit_cell.yz, 0.0)
+
+    def test_dimensions(self):
+        lattice_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 0]])
+        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors, dimensions=2)
+        assert unit_cell.dimensions == 2
+        assert np.isclose(unit_cell.Lz, 0)
+
     def test_matrix(self):
         box = freud.box.Box(2, 2, 2, 1, 0.5, 0.1)
         box2 = freud.box.Box.from_matrix(box.to_matrix())

From 7706c2f4ccc428a8d79cccd8ac6244ab85cc5bd3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 20 Mar 2024 13:35:46 +0000
Subject: [PATCH 11/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 freud/box.pyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 4d8c0a8a9..e89778b75 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -702,7 +702,7 @@ cdef class Box:
         beta = np.arccos(self.xz/np.sqrt(1+self.xz**2+self.yz**2))
         gamma = np.arccos(self.xy/np.sqrt(1+self.xy**2))
         L1 = self.Lx
-        a2 = [self.Ly*self.xy, self.Ly,0] 
+        a2 = [self.Ly*self.xy, self.Ly,0]
         a3 = [self.Lz*self.xz, self.Lz*self.yz, self.Lz]
         L2 = np.linalg.norm(a2)
         L3 = np.linalg.norm(a3)
@@ -947,7 +947,7 @@ cdef class Box:
         Args:
             lattice_vectors (array-like):
                 The lattice vectors. The dimensions of the object should be 3x3. Lattice
-                vector a1 is lattice_vectors[:, 0], etc. 
+                vector a1 is lattice_vectors[:, 0], etc.
             dimensions (int): The number of dimensions (Default value = :code:`None`)
 
         Returns:

From 88609618cc560880ba32ddc9d60bb3877a101e83 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 14:36:09 +0100
Subject: [PATCH 12/37] update some docstrings for consistency

---
 freud/box.pyx |  2 +-
 freud/data.py | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 4d8c0a8a9..9443548e2 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -947,7 +947,7 @@ cdef class Box:
         Args:
             lattice_vectors (array-like):
                 The lattice vectors. The dimensions of the object should be 3x3. Lattice
-                vector a1 is lattice_vectors[:, 0], etc. 
+                vector a1 is lattice_vectors[0], etc. 
             dimensions (int): The number of dimensions (Default value = :code:`None`)
 
         Returns:
diff --git a/freud/data.py b/freud/data.py
index 98624d34d..aa5261c2a 100644
--- a/freud/data.py
+++ b/freud/data.py
@@ -241,7 +241,7 @@ def from_lattice_vectors(
 
         Args:
             lattice_vectors (:math:`(3, 3)` :class:`np.ndarray
-                The lattice vectors. Lattice vector a1 is lattice_vectors[:, 0], etc.
+                The lattice vectors. Lattice vector a1 is lattice_vectors[0], etc.
             unique_positions (:math:`(N_{points}, 3)` :class:`np.ndarray`):
                 The basis positions.
 
@@ -255,9 +255,9 @@ def from_lattice_vectors(
     @classmethod
     def from_box_lengths_and_angles(
         cls,
-        Lx: float,
-        Ly: float,
-        Lz: float,
+        L1: float,
+        L2: float,
+        L3: float,
         alpha: float,
         beta: float,
         gamma: float,
@@ -266,9 +266,9 @@ def from_box_lengths_and_angles(
         """Create a unit cell from box lengths and angles.
 
         Args:
-            Lx (float): The length of the box in the x direction.
-            Ly (float): The length of the box in the y direction.
-            Lz (float): The length of the box in the z direction.
+            L1 (float): The length of the first box vector.
+            L2 (float): The length of the second box vector.
+            L3 (float): The length of the third box vector.
             alpha (float): The angle between the x and y lattice vectors.
             beta (float): The angle between the x and z lattice vectors.
             gamma (float): The angle between the y and z lattice vectors.
@@ -279,7 +279,7 @@ def from_box_lengths_and_angles(
             :class:`~.UnitCell`: A unit cell with the given box lengths and angles.
         """
         return cls(
-            freud.box.Box.from_box_lengths_and_angles(Lx, Ly, Lz, alpha, beta, gamma),
+            freud.box.Box.from_box_lengths_and_angles(L1, L2, L3, alpha, beta, gamma),
             unique_positions,
         )
 

From 0e78e470247aa0792173e4b73b7beb73fbaacf8e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 20 Mar 2024 13:37:58 +0000
Subject: [PATCH 13/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 freud/box.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 9febc6353..2c365150d 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -947,7 +947,7 @@ cdef class Box:
         Args:
             lattice_vectors (array-like):
                 The lattice vectors. The dimensions of the object should be 3x3. Lattice
-                vector a1 is lattice_vectors[0], etc. 
+                vector a1 is lattice_vectors[0], etc.
             dimensions (int): The number of dimensions (Default value = :code:`None`)
 
         Returns:

From da9d7eab48bbc63893bd16212a074d1fcdc5d417 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 14:39:50 +0100
Subject: [PATCH 14/37] linter fix

---
 freud/box.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 2c365150d..0cdbcf7dd 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -702,7 +702,7 @@ cdef class Box:
         beta = np.arccos(self.xz/np.sqrt(1+self.xz**2+self.yz**2))
         gamma = np.arccos(self.xy/np.sqrt(1+self.xy**2))
         L1 = self.Lx
-        a2 = [self.Ly*self.xy, self.Ly,0]
+        a2 = [self.Ly*self.xy, self.Ly, 0]
         a3 = [self.Lz*self.xz, self.Lz*self.yz, self.Lz]
         L2 = np.linalg.norm(a2)
         L3 = np.linalg.norm(a3)

From aa4354a469bbfdda2729ce3b2903a920f9505b2f Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Wed, 20 Mar 2024 14:50:33 +0100
Subject: [PATCH 15/37] added changelog and credits

---
 ChangeLog.md                     | 4 ++++
 doc/source/reference/credits.rst | 7 +++++++
 2 files changed, 11 insertions(+)

diff --git a/ChangeLog.md b/ChangeLog.md
index 11dc46e34..6e11233d1 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -8,6 +8,10 @@ and this project adheres to
 
 ### Added
 * New continuous coordination number compute `freud.order.ContinuousCoordination`.
+* New class methods for construction of `freud.box.Box` and `freud.data.UnitCell` from
+  lattice vectors and box lengths and angles.
+* New `freud.box.Box.to_box_lengths_and_angles` method for computing box vector lengths
+  and angles 
 
 ### Removed
 * `freud.order.Translational`.
diff --git a/doc/source/reference/credits.rst b/doc/source/reference/credits.rst
index 46d811605..3ba7af49d 100644
--- a/doc/source/reference/credits.rst
+++ b/doc/source/reference/credits.rst
@@ -369,6 +369,13 @@ Domagoj Fijan
 * Contributed code, design, documentation, and testing for ``freud.locality.FilterSANN`` class.
 * Contributed code, design, documentation, and testing for ``freud.locality.FilterRAD`` class.
 * Added support for ``gsd.hoomd.Frame`` in ``NeighborQuery.from_system`` calls.
+* Added support for ``freud.box.Box`` class methods for construction of boxes and unit
+  cells from lattice vectors (``freud.box.Box.from_lattice_vectors`` and
+  ``freud.data.UnitCell.from_lattice_vectors``) and cell lengths and angles
+  (``freud.box.Box.from_box_lengths_and_angles`` and
+  ``freud.data.UnitCell.from_box_lengths_and_angles``), as well as a method for
+  returning cell vector lengths and angles 
+  (``freud.box.Box.to_box_lengths_and_angles``).
 
 Andrew Kerr
 

From d5369858486001ac90c1ff7e73b1ff6a848a90cb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 20 Mar 2024 13:50:53 +0000
Subject: [PATCH 16/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 ChangeLog.md                     | 2 +-
 doc/source/reference/credits.rst | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ChangeLog.md b/ChangeLog.md
index 6e11233d1..1f5aa99e7 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -11,7 +11,7 @@ and this project adheres to
 * New class methods for construction of `freud.box.Box` and `freud.data.UnitCell` from
   lattice vectors and box lengths and angles.
 * New `freud.box.Box.to_box_lengths_and_angles` method for computing box vector lengths
-  and angles 
+  and angles
 
 ### Removed
 * `freud.order.Translational`.
diff --git a/doc/source/reference/credits.rst b/doc/source/reference/credits.rst
index 3ba7af49d..06eeae5b4 100644
--- a/doc/source/reference/credits.rst
+++ b/doc/source/reference/credits.rst
@@ -374,7 +374,7 @@ Domagoj Fijan
   ``freud.data.UnitCell.from_lattice_vectors``) and cell lengths and angles
   (``freud.box.Box.from_box_lengths_and_angles`` and
   ``freud.data.UnitCell.from_box_lengths_and_angles``), as well as a method for
-  returning cell vector lengths and angles 
+  returning cell vector lengths and angles
   (``freud.box.Box.to_box_lengths_and_angles``).
 
 Andrew Kerr

From 461485ed2ffd68945915911c5ab8b1f13448f160 Mon Sep 17 00:00:00 2001
From: janbridley <bradleyjenj@gmail.com>
Date: Wed, 20 Mar 2024 11:30:06 -0400
Subject: [PATCH 17/37] Test dimension detection for `from_lattice_vectors`

---
 tests/test_box_Box.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index a613ffdf1..69a3f8cf2 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -536,9 +536,10 @@ def test_tilted_lattice(self):
         assert np.isclose(unit_cell.xz, 0.0)
         assert np.isclose(unit_cell.yz, 0.0)
 
-    def test_dimensions(self):
+    @pytest.mark.parametrize("dim", [2, None])
+    def test_dimensions(self, dim):
         lattice_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 0]])
-        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors, dimensions=2)
+        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors, dimensions=dim)
         assert unit_cell.dimensions == 2
         assert np.isclose(unit_cell.Lz, 0)
 

From 90dd30c53f703e4ff005bd2513040f837d54c423 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <50439291+DomFijan@users.noreply.github.com>
Date: Thu, 21 Mar 2024 18:42:18 +0100
Subject: [PATCH 18/37] Update freud/box.pyx

Co-authored-by: Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>
---
 freud/box.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 0cdbcf7dd..fdfc63a71 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -693,7 +693,7 @@ cdef class Box:
         r"""Return the box lengths and angles.
 
         Returns:
-            tuple: The box vector lengths and angles in radians
+            tuple: The box vector lengths and angles in radians :math:`(L_1, L_2, L_3, \alpha, \beta, \gamma)`.
         """
         alpha = np.arccos(
             (self.xy * self.xz + self.yz)

From 8e27b3c001d3332a96acf5fa230ac7d994f48a07 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 21 Mar 2024 18:42:41 +0100
Subject: [PATCH 19/37] apply requested changes

---
 freud/box.pyx | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 0cdbcf7dd..7aa4b394d 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -977,13 +977,13 @@ cdef class Box:
     @classmethod
     def from_box_lengths_and_angles(
         cls,
-        L1: float,
-        L2: float,
-        L3: float,
-        alpha: float,
-        beta: float,
-        gamma: float,
-        dimensions: int = None,
+        L1,
+        L2,
+        L3,
+        alpha,
+        beta,
+        gamma,
+        dimensions = None,
     ):
         r"""Construct a box from lengths and angles.
 
@@ -991,9 +991,9 @@ cdef class Box:
             L1 (float): The length of the first lattice vector
             L2 (float): The length of the second lattice vector
             L3 (float): The length of the third lattice vector
-            alpha (float): The angle between the y and z axes in radians
-            beta (float): The angle between the x and z axes in radians
-            gamma (float): The angle between the x and y axes in radians
+            alpha (float): The angle between second and third lattice vector in radians
+            beta (float): The angle between first and third lattice vector in radians
+            gamma (float): The angle between the first and second lattice vector in radians
             dimensions (int): The number of dimensions (Default value = :code:`None`)
 
         Returns:

From 5bd2c0813d6390e36c4622e513aadec2cceb1aad Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 21 Mar 2024 19:01:06 +0100
Subject: [PATCH 20/37] revert unwanted changes and delete tests

---
 freud/box.pyx         | 45 +++-----------------------------------
 freud/data.py         | 50 -------------------------------------------
 tests/test_box_Box.py | 35 ------------------------------
 3 files changed, 3 insertions(+), 127 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index c18a6d9c3..3f2947489 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -693,7 +693,8 @@ cdef class Box:
         r"""Return the box lengths and angles.
 
         Returns:
-            tuple: The box vector lengths and angles in radians :math:`(L_1, L_2, L_3, \alpha, \beta, \gamma)`.
+            tuple: The box vector lengths and angles in radians
+            :math:`(L_1, L_2, L_3, \alpha, \beta, \gamma)`.
         """
         alpha = np.arccos(
             (self.xy * self.xz + self.yz)
@@ -940,50 +941,10 @@ cdef class Box:
                             "positional argument: L")
         return cls(Lx=L, Ly=L, Lz=0, xy=0, xz=0, yz=0, is2D=True)
 
-    @classmethod
-    def from_lattice_vectors(cls, lattice_vectors, dimensions: int = None):
-        """Create a unit cell from lattice vectors.
-
-        Args:
-            lattice_vectors (array-like):
-                The lattice vectors. The dimensions of the object should be 3x3. Lattice
-                vector a1 is lattice_vectors[0], etc.
-            dimensions (int): The number of dimensions (Default value = :code:`None`)
-
-        Returns:
-            :class:`~.UnitCell`: A unit cell with the given lattice vectors.
-        """
-        lattice_matrix = np.asarray(lattice_vectors, dtype=np.float32)
-        v0 = lattice_matrix[0]
-        v1 = lattice_matrix[1]
-        v2 = lattice_matrix[2]
-        Lx = np.sqrt(np.dot(v0, v0))
-        a2x = np.dot(v0, v1) / Lx
-        Ly = np.sqrt(np.dot(v1, v1) - a2x * a2x)
-        xy = a2x / Ly
-        v0xv1 = np.cross(v0, v1)
-        v0xv1mag = np.sqrt(np.dot(v0xv1, v0xv1))
-        Lz = np.dot(v2, v0xv1) / v0xv1mag
-        if Lz != 0:
-            a3x = np.dot(v0, v2) / Lx
-            xz = a3x / Lz
-            yz = (np.dot(v1, v2) - a2x * a3x) / (Ly * Lz)
-        else:
-            xz = yz = 0
-        if dimensions is None:
-            dimensions = 2 if Lz == 0 else 3
-        return cls.from_box([Lx, Ly, Lz, xy, xz, yz], dimensions=dimensions)
 
     @classmethod
     def from_box_lengths_and_angles(
-        cls,
-        L1,
-        L2,
-        L3,
-        alpha,
-        beta,
-        gamma,
-        dimensions = None,
+        cls, L1, L2, L3, alpha, beta, gamma, dimensions = None,
     ):
         r"""Construct a box from lengths and angles.
 
diff --git a/freud/data.py b/freud/data.py
index aa5261c2a..87c0c0bfb 100644
--- a/freud/data.py
+++ b/freud/data.py
@@ -233,56 +233,6 @@ def hex(cls):
         fractions = np.array([[0, 0, 0], [0.5, 0.5, 0]])
         return cls([1, np.sqrt(3)], fractions)
 
-    @classmethod
-    def from_lattice_vectors(
-        cls, lattice_vectors: np.ndarray, unique_positions: np.ndarray
-    ):
-        """Create a unit cell from lattice vectors.
-
-        Args:
-            lattice_vectors (:math:`(3, 3)` :class:`np.ndarray
-                The lattice vectors. Lattice vector a1 is lattice_vectors[0], etc.
-            unique_positions (:math:`(N_{points}, 3)` :class:`np.ndarray`):
-                The basis positions.
-
-        Returns:
-            :class:`~.UnitCell`: A unit cell with the given lattice vectors.
-        """
-        return cls(
-            freud.box.Box.from_lattice_vectors(lattice_vectors), unique_positions
-        )
-
-    @classmethod
-    def from_box_lengths_and_angles(
-        cls,
-        L1: float,
-        L2: float,
-        L3: float,
-        alpha: float,
-        beta: float,
-        gamma: float,
-        unique_positions: np.ndarray,
-    ):
-        """Create a unit cell from box lengths and angles.
-
-        Args:
-            L1 (float): The length of the first box vector.
-            L2 (float): The length of the second box vector.
-            L3 (float): The length of the third box vector.
-            alpha (float): The angle between the x and y lattice vectors.
-            beta (float): The angle between the x and z lattice vectors.
-            gamma (float): The angle between the y and z lattice vectors.
-            unique_positions (:math:`(N_{points}, 3)` :class:`np.ndarray
-                The basis positions.
-
-        Returns:
-            :class:`~.UnitCell`: A unit cell with the given box lengths and angles.
-        """
-        return cls(
-            freud.box.Box.from_box_lengths_and_angles(L1, L2, L3, alpha, beta, gamma),
-            unique_positions,
-        )
-
 
 def make_random_system(box_size, num_points, is2D=False, seed=None):
     r"""Helper function to make random points with a cubic or square box.
diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index 69a3f8cf2..fca40e6b3 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -507,41 +507,6 @@ def test_to_and_from_box_lengths_and_angles(self):
         lengths_and_angles_computed = box.to_box_lengths_and_angles()
         assert np.allclose(lengths_and_angles_computed, original_box_lengths_and_angles)
 
-    def test_from_lattice_vectors_cubic_lattice(self):
-        lattice_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
-        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors)
-        assert unit_cell.Lx == 1
-        assert unit_cell.Ly == 1
-        assert unit_cell.Lz == 1
-        assert unit_cell.xy == 0
-        assert unit_cell.xz == 0
-        assert unit_cell.yz == 0
-
-    def test_from_lattice_vectors_non_cubic_lattice(self):
-        box = freud.box.Box.from_lattice_vectors([[1, 0, 0], [0, 2, 0], [0, 0, 3]])
-        assert box.Lx == 1
-        assert box.Ly == 2
-        assert box.Lz == 3
-        assert box.xy == 0
-        assert box.xz == 0
-        assert box.yz == 0
-
-    def test_tilted_lattice(self):
-        lattice_vectors = np.array([[1, 0, 0], [0.5, np.sqrt(3) / 2, 0], [0, 0, 1]])
-        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors)
-        assert np.isclose(unit_cell.Lx, 1.0)
-        assert np.isclose(unit_cell.Ly, np.sqrt(3) / 2)
-        assert np.isclose(unit_cell.Lz, 1.0)
-        assert np.isclose(unit_cell.xy, np.sqrt(3) / 3)
-        assert np.isclose(unit_cell.xz, 0.0)
-        assert np.isclose(unit_cell.yz, 0.0)
-
-    @pytest.mark.parametrize("dim", [2, None])
-    def test_dimensions(self, dim):
-        lattice_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 0]])
-        unit_cell = freud.box.Box.from_lattice_vectors(lattice_vectors, dimensions=dim)
-        assert unit_cell.dimensions == 2
-        assert np.isclose(unit_cell.Lz, 0)
 
     def test_matrix(self):
         box = freud.box.Box(2, 2, 2, 1, 0.5, 0.1)

From 6a9b7408a6890509b305de9ecb8810d3be3ca4a9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Mar 2024 18:01:29 +0000
Subject: [PATCH 21/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_box_Box.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index fca40e6b3..dbb881f7b 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -507,7 +507,6 @@ def test_to_and_from_box_lengths_and_angles(self):
         lengths_and_angles_computed = box.to_box_lengths_and_angles()
         assert np.allclose(lengths_and_angles_computed, original_box_lengths_and_angles)
 
-
     def test_matrix(self):
         box = freud.box.Box(2, 2, 2, 1, 0.5, 0.1)
         box2 = freud.box.Box.from_matrix(box.to_matrix())

From 1a45db106d9397cfb45e34134a14782bfe46720e Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 21 Mar 2024 19:03:19 +0100
Subject: [PATCH 22/37] fix format

---
 freud/box.pyx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 3f2947489..e381a94b5 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -941,10 +941,9 @@ cdef class Box:
                             "positional argument: L")
         return cls(Lx=L, Ly=L, Lz=0, xy=0, xz=0, yz=0, is2D=True)
 
-
     @classmethod
     def from_box_lengths_and_angles(
-        cls, L1, L2, L3, alpha, beta, gamma, dimensions = None,
+        cls, L1, L2, L3, alpha, beta, gamma, dimensions=None,
     ):
         r"""Construct a box from lengths and angles.
 

From ace7fac122df817f205f543f2dd30662ff8cd463 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 21 Mar 2024 19:06:57 +0100
Subject: [PATCH 23/37] final format fix

---
 freud/box.pyx | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index e381a94b5..6b0e44fdf 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -693,8 +693,9 @@ cdef class Box:
         r"""Return the box lengths and angles.
 
         Returns:
-            tuple: The box vector lengths and angles in radians
-            :math:`(L_1, L_2, L_3, \alpha, \beta, \gamma)`.
+            tuple: 
+                The box vector lengths and angles in radians
+                :math:`(L_1, L_2, L_3, \alpha, \beta, \gamma)`.
         """
         alpha = np.arccos(
             (self.xy * self.xz + self.yz)
@@ -948,13 +949,20 @@ cdef class Box:
         r"""Construct a box from lengths and angles.
 
         Args:
-            L1 (float): The length of the first lattice vector
-            L2 (float): The length of the second lattice vector
-            L3 (float): The length of the third lattice vector
-            alpha (float): The angle between second and third lattice vector in radians
-            beta (float): The angle between first and third lattice vector in radians
-            gamma (float): The angle between the first and second lattice vector in radians
-            dimensions (int): The number of dimensions (Default value = :code:`None`)
+            L1 (float):
+                The length of the first lattice vector
+            L2 (float):
+                The length of the second lattice vector
+            L3 (float):
+                The length of the third lattice vector
+            alpha (float):
+                The angle between second and third lattice vector in radians
+            beta (float): 
+                The angle between first and third lattice vector in radians
+            gamma (float): 
+                The angle between the first and second lattice vector in radians
+            dimensions (int):
+                The number of dimensions (Default value = :code:`None`)
 
         Returns:
             :class:`freud.box.Box`: The resulting box object.

From 6f6932e5ee411286cda52104cd30305c734a22f3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Mar 2024 18:08:03 +0000
Subject: [PATCH 24/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 freud/box.pyx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 6b0e44fdf..aed409b24 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -693,7 +693,7 @@ cdef class Box:
         r"""Return the box lengths and angles.
 
         Returns:
-            tuple: 
+            tuple:
                 The box vector lengths and angles in radians
                 :math:`(L_1, L_2, L_3, \alpha, \beta, \gamma)`.
         """
@@ -957,9 +957,9 @@ cdef class Box:
                 The length of the third lattice vector
             alpha (float):
                 The angle between second and third lattice vector in radians
-            beta (float): 
+            beta (float):
                 The angle between first and third lattice vector in radians
-            gamma (float): 
+            gamma (float):
                 The angle between the first and second lattice vector in radians
             dimensions (int):
                 The number of dimensions (Default value = :code:`None`)

From ae9683628a2797afd6a85b160cdd7ea3fe74c604 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 21 Mar 2024 19:52:26 +0100
Subject: [PATCH 25/37] fix from_box_lengths_and_angles

---
 freud/box.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index aed409b24..0450b4a85 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -975,7 +975,7 @@ cdef class Box:
         a3 = np.array([L3 * a3x, L3 * a3y, L3 * a3z])
         if dimensions is None:
             dimensions = 2 if L3 == 0 else 3
-        return cls.from_lattice_vectors(np.array([a1, a2, a3]), dimensions=dimensions)
+        return cls.from_matrix(np.array([a1, a2, a3]).T, dimensions=dimensions)
 
 
 cdef BoxFromCPP(const freud._box.Box & cppbox):

From 3aab7cb3ca64314321b98048b0cfe7c3db0fe239 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 21 Mar 2024 19:56:20 +0100
Subject: [PATCH 26/37] fix changelog and credits

---
 ChangeLog.md                     | 5 ++---
 doc/source/reference/credits.rst | 9 +++------
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/ChangeLog.md b/ChangeLog.md
index 1f5aa99e7..21d87cb66 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -8,10 +8,9 @@ and this project adheres to
 
 ### Added
 * New continuous coordination number compute `freud.order.ContinuousCoordination`.
-* New class methods for construction of `freud.box.Box` and `freud.data.UnitCell` from
-  lattice vectors and box lengths and angles.
+* New class methods for construction of `freud.box.Box` from box lengths and angles.
 * New `freud.box.Box.to_box_lengths_and_angles` method for computing box vector lengths
-  and angles
+  and angles.
 
 ### Removed
 * `freud.order.Translational`.
diff --git a/doc/source/reference/credits.rst b/doc/source/reference/credits.rst
index 06eeae5b4..415f88fa8 100644
--- a/doc/source/reference/credits.rst
+++ b/doc/source/reference/credits.rst
@@ -369,12 +369,9 @@ Domagoj Fijan
 * Contributed code, design, documentation, and testing for ``freud.locality.FilterSANN`` class.
 * Contributed code, design, documentation, and testing for ``freud.locality.FilterRAD`` class.
 * Added support for ``gsd.hoomd.Frame`` in ``NeighborQuery.from_system`` calls.
-* Added support for ``freud.box.Box`` class methods for construction of boxes and unit
-  cells from lattice vectors (``freud.box.Box.from_lattice_vectors`` and
-  ``freud.data.UnitCell.from_lattice_vectors``) and cell lengths and angles
-  (``freud.box.Box.from_box_lengths_and_angles`` and
-  ``freud.data.UnitCell.from_box_lengths_and_angles``), as well as a method for
-  returning cell vector lengths and angles
+* Added support for ``freud.box.Box`` class methods for construction of boxes from cell
+  lengths and angles (``freud.box.Box.from_box_lengths_and_angles``), as well as a
+  method for returning box vector lengths and angles
   (``freud.box.Box.to_box_lengths_and_angles``).
 
 Andrew Kerr

From a7c18e2ae8574c34f96f6adc4d587a92ec176eb6 Mon Sep 17 00:00:00 2001
From: Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>
Date: Thu, 21 Mar 2024 16:37:56 -0400
Subject: [PATCH 27/37] Update freud/box.pyx

---
 freud/box.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 0450b4a85..dcbd70c40 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -962,7 +962,7 @@ cdef class Box:
             gamma (float):
                 The angle between the first and second lattice vector in radians
             dimensions (int):
-                The number of dimensions (Default value = :code:`None`)
+                The number of dimensions (Default value = :code:`None`).
 
         Returns:
             :class:`freud.box.Box`: The resulting box object.

From c26e88e38662e912d94727e30b9c6a9e5f53c384 Mon Sep 17 00:00:00 2001
From: Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>
Date: Thu, 21 Mar 2024 16:38:43 -0400
Subject: [PATCH 28/37] Apply suggestions from code review

---
 freud/box.pyx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index dcbd70c40..c0d10613d 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -950,17 +950,17 @@ cdef class Box:
 
         Args:
             L1 (float):
-                The length of the first lattice vector
+                The length of the first lattice vector.
             L2 (float):
-                The length of the second lattice vector
+                The length of the second lattice vector.
             L3 (float):
-                The length of the third lattice vector
+                The length of the third lattice vector.
             alpha (float):
-                The angle between second and third lattice vector in radians
+                The angle between second and third lattice vector in radians.
             beta (float):
-                The angle between first and third lattice vector in radians
+                The angle between first and third lattice vector in radians.
             gamma (float):
-                The angle between the first and second lattice vector in radians
+                The angle between the first and second lattice vector in radians.
             dimensions (int):
                 The number of dimensions (Default value = :code:`None`).
 

From ae56eff6e150548aa72b54e1d15b913189275f46 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <50439291+DomFijan@users.noreply.github.com>
Date: Fri, 22 Mar 2024 10:56:49 +0100
Subject: [PATCH 29/37] Update ChangeLog.md

Co-authored-by: Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>
---
 ChangeLog.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/ChangeLog.md b/ChangeLog.md
index 21d87cb66..5b27e681b 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -8,9 +8,7 @@ and this project adheres to
 
 ### Added
 * New continuous coordination number compute `freud.order.ContinuousCoordination`.
-* New class methods for construction of `freud.box.Box` from box lengths and angles.
-* New `freud.box.Box.to_box_lengths_and_angles` method for computing box vector lengths
-  and angles.
+* New methods for conversion of box lengths and angles to/from `freud.box.Box`.
 
 ### Removed
 * `freud.order.Translational`.

From a3daf1b58016dbdc7fe83499951540bfa2573e96 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Fri, 22 Mar 2024 11:29:32 +0100
Subject: [PATCH 30/37] update docs to state range of angles allowed

---
 freud/box.pyx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/freud/box.pyx b/freud/box.pyx
index c0d10613d..eb1030d45 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -948,6 +948,8 @@ cdef class Box:
     ):
         r"""Construct a box from lengths and angles.
 
+        All the angles provided must be between 0 and :math:`\pi`.
+
         Args:
             L1 (float):
                 The length of the first lattice vector.

From dffb7725f306366a4a1762113a370e56d6bb4836 Mon Sep 17 00:00:00 2001
From: Tommy Waltmann <tomwalt@umich.edu>
Date: Fri, 22 Mar 2024 09:56:06 -0400
Subject: [PATCH 31/37] update test

---
 tests/test_box_Box.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index dbb881f7b..7b19909ef 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -494,18 +494,19 @@ def test_standard_orthogonal_box(self):
 
     def test_to_and_from_box_lengths_and_angles(self):
         original_box_lengths_and_angles = (
-            1,
-            2,
-            3,
-            np.pi / 3,
-            np.pi / 2.25,
-            np.pi / 2.35,
+            np.random.uniform(0, 100000),
+            np.random.uniform(0, 100000),
+            np.random.uniform(0, 100000),
+            np.random.uniform(0, np.pi),
+            np.random.uniform(0, np.pi),
+            np.random.uniform(0, np.pi),
         )
         box = freud.box.Box.from_box_lengths_and_angles(
             *original_box_lengths_and_angles
         )
         lengths_and_angles_computed = box.to_box_lengths_and_angles()
-        assert np.allclose(lengths_and_angles_computed, original_box_lengths_and_angles)
+        np.testing.assert_allclose(lengths_and_angles_computed,
+                                   original_box_lengths_and_angles, rtol=1e-6)
 
     def test_matrix(self):
         box = freud.box.Box(2, 2, 2, 1, 0.5, 0.1)

From a3548a12a82a666e42c80d4f9dfa6acbde7f7c76 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 22 Mar 2024 13:56:31 +0000
Subject: [PATCH 32/37] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_box_Box.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index 7b19909ef..3fba3f423 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -505,8 +505,9 @@ def test_to_and_from_box_lengths_and_angles(self):
             *original_box_lengths_and_angles
         )
         lengths_and_angles_computed = box.to_box_lengths_and_angles()
-        np.testing.assert_allclose(lengths_and_angles_computed,
-                                   original_box_lengths_and_angles, rtol=1e-6)
+        np.testing.assert_allclose(
+            lengths_and_angles_computed, original_box_lengths_and_angles, rtol=1e-6
+        )
 
     def test_matrix(self):
         box = freud.box.Box(2, 2, 2, 1, 0.5, 0.1)

From a3449d8f99e0c86a44c94412be0fc9d8205a3ecd Mon Sep 17 00:00:00 2001
From: janbridley <bradleyjenj@gmail.com>
Date: Tue, 26 Mar 2024 14:01:00 -0400
Subject: [PATCH 33/37] Set nonzero atol for assert_allclose in test_box_Box.py

---
 tests/test_box_Box.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index 3fba3f423..f6f583e88 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -506,7 +506,10 @@ def test_to_and_from_box_lengths_and_angles(self):
         )
         lengths_and_angles_computed = box.to_box_lengths_and_angles()
         np.testing.assert_allclose(
-            lengths_and_angles_computed, original_box_lengths_and_angles, rtol=1e-6
+            lengths_and_angles_computed,
+            original_box_lengths_and_angles,
+            rtol=1e-6,
+            atol=1e-14,
         )
 
     def test_matrix(self):

From ca710c330b345458bc8b548bae143e432b7e6930 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 11 Apr 2024 18:03:05 -0400
Subject: [PATCH 34/37] update from_box_lengths_and_angles docstring to contain
 restrictions for angles and raise valueerror when violated

---
 freud/box.pyx | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index eb1030d45..82fe5d6db 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -946,7 +946,7 @@ cdef class Box:
     def from_box_lengths_and_angles(
         cls, L1, L2, L3, alpha, beta, gamma, dimensions=None,
     ):
-        r"""Construct a box from lengths and angles.
+        r"""Construct a box from lengths and angles (in radians).
 
         All the angles provided must be between 0 and :math:`\pi`.
 
@@ -958,17 +958,26 @@ cdef class Box:
             L3 (float):
                 The length of the third lattice vector.
             alpha (float):
-                The angle between second and third lattice vector in radians.
+                The angle between second and third lattice vector in radians (must be
+                between 0 and :math:`\pi`).
             beta (float):
-                The angle between first and third lattice vector in radians.
+                The angle between first and third lattice vector in radians (must be
+                between 0 and :math:`\pi`).
             gamma (float):
-                The angle between the first and second lattice vector in radians.
+                The angle between the first and second lattice vector in radians (must
+                be between 0 and :math:`\pi`).
             dimensions (int):
                 The number of dimensions (Default value = :code:`None`).
 
         Returns:
             :class:`freud.box.Box`: The resulting box object.
         """
+        if not 0 < alpha < np.pi:
+            raise ValueError("alpha must be between 0 and pi.")
+        if not 0 < beta < np.pi:
+            raise ValueError("beta must be between 0 and pi.")
+        if not 0 < gamma < np.pi:
+            raise ValueError("gamma must be between 0 and pi.")
         a1 = np.array([L1, 0, 0])
         a2 = np.array([L2 * np.cos(gamma), L2 * np.sin(gamma), 0])
         a3x = np.cos(beta)

From ad8d8b3b692c01ea6ae5a050683cd13030f526ac Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 11 Apr 2024 19:16:17 -0400
Subject: [PATCH 35/37] raise error if box has negative volume

---
 freud/box.pyx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 82fe5d6db..1b12fbcae 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -982,7 +982,10 @@ cdef class Box:
         a2 = np.array([L2 * np.cos(gamma), L2 * np.sin(gamma), 0])
         a3x = np.cos(beta)
         a3y = (np.cos(alpha) - np.cos(beta) * np.cos(gamma)) / np.sin(gamma)
-        a3z = np.sqrt(1 - a3x**2 - a3y**2)
+        under_sqrt = 1 - a3x**2 - a3y**2
+        if under_sqrt < 0:
+            raise ValueError("The provided angles can not form a valid box.")
+        a3z = np.sqrt()
         a3 = np.array([L3 * a3x, L3 * a3y, L3 * a3z])
         if dimensions is None:
             dimensions = 2 if L3 == 0 else 3

From b51d8d74df90a063cdd51cf609d613af599d47a3 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Thu, 11 Apr 2024 19:16:36 -0400
Subject: [PATCH 36/37] fix sqrt

---
 freud/box.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/freud/box.pyx b/freud/box.pyx
index 1b12fbcae..f72151bbf 100644
--- a/freud/box.pyx
+++ b/freud/box.pyx
@@ -985,7 +985,7 @@ cdef class Box:
         under_sqrt = 1 - a3x**2 - a3y**2
         if under_sqrt < 0:
             raise ValueError("The provided angles can not form a valid box.")
-        a3z = np.sqrt()
+        a3z = np.sqrt(under_sqrt)
         a3 = np.array([L3 * a3x, L3 * a3y, L3 * a3z])
         if dimensions is None:
             dimensions = 2 if L3 == 0 else 3

From d78e08e9b7c273910432f1b8bd734ef8752fd920 Mon Sep 17 00:00:00 2001
From: Domagoj Fijan <domagoj.fijan@gmail.com>
Date: Tue, 23 Apr 2024 12:00:55 -0400
Subject: [PATCH 37/37] fix test to check for imposible boxes

---
 tests/test_box_Box.py | 39 +++++++++++++++++++++++++++++----------
 1 file changed, 29 insertions(+), 10 deletions(-)

diff --git a/tests/test_box_Box.py b/tests/test_box_Box.py
index f6f583e88..c810925b9 100644
--- a/tests/test_box_Box.py
+++ b/tests/test_box_Box.py
@@ -501,16 +501,35 @@ def test_to_and_from_box_lengths_and_angles(self):
             np.random.uniform(0, np.pi),
             np.random.uniform(0, np.pi),
         )
-        box = freud.box.Box.from_box_lengths_and_angles(
-            *original_box_lengths_and_angles
-        )
-        lengths_and_angles_computed = box.to_box_lengths_and_angles()
-        np.testing.assert_allclose(
-            lengths_and_angles_computed,
-            original_box_lengths_and_angles,
-            rtol=1e-6,
-            atol=1e-14,
-        )
+        if (
+            1
+            - np.cos(original_box_lengths_and_angles[4]) ** 2
+            - (
+                (
+                    np.cos(original_box_lengths_and_angles[3])
+                    - np.cos(original_box_lengths_and_angles[4])
+                    * np.cos(original_box_lengths_and_angles[5])
+                )
+                / np.sin(original_box_lengths_and_angles[5])
+            )
+            ** 2
+            < 0
+        ):
+            with pytest.raises(ValueError):
+                freud.box.Box.from_box_lengths_and_angles(
+                    *original_box_lengths_and_angles
+                )
+        else:
+            box = freud.box.Box.from_box_lengths_and_angles(
+                *original_box_lengths_and_angles
+            )
+            lengths_and_angles_computed = box.to_box_lengths_and_angles()
+            np.testing.assert_allclose(
+                lengths_and_angles_computed,
+                original_box_lengths_and_angles,
+                rtol=1e-6,
+                atol=1e-14,
+            )
 
     def test_matrix(self):
         box = freud.box.Box(2, 2, 2, 1, 0.5, 0.1)