amepproject · hechtprojects · Mar 9, 2025 · Dec 6, 2024 · Dec 6, 2024 · Feb 24, 2025
diff --git a/amep/cluster.py b/amep/cluster.py
@@ -383,10 +383,10 @@ def radius_of_gyration(
 
     Notes:
     ------
-    For a cluster composed of $n$ particles of masses $m_i, i=1,2, \ldots, n$, 
-    located at fixed distances $s_i$ from the centre of mass, the radius of gyration is 
-    the square-root of the mass average of $s_i^2$ over all mass elements, i.e.,
-    $R_g=\left(\sum_{i=1}^n m_i s_i^2 / \sum_{i=1}^n m_i\right)^{1 / 2}$
+    For a cluster composed of :math:`n` particles of masses :math:`m_i, i=1,2, \ldots, n`, 
+    located at fixed distances :math:`s_i` from the centre of mass, the radius of gyration is 
+    the square-root of the mass average of :math:`s_i^2` over all mass elements, i.e.,
+    :math:`R_g=\left(\sum_{i=1}^n m_i s_i^2 / \sum_{i=1}^n m_i\right)^{1 / 2}`.
 
     Parameters:
     -----------

diff --git a/amep/continuum.py b/amep/continuum.py
@@ -155,7 +155,7 @@ def sf2d(
     .. math::
         S(\vec{q}) = <\rho(\vec{q})\rho(\vec{-q})>= <|\rho(\vec{q})|^2>,
 
-    where $\rho(\vec{q})$ is the Fourier transform of the particle number
+    where :math:`\rho(\vec{q})` is the Fourier transform of the particle number
     density (see Ref. [1]_ [2]_ [3]_ for further information).
 
     .. [1] Hansen, J.-P., & McDonald, I. R. (2006). Theory of Simple Liquids

diff --git a/amep/evaluate.py b/amep/evaluate.py
@@ -1408,7 +1408,7 @@ def __init__(
             S_{2D}(q) = \frac{1}{N}\left\langle\sum_{m,l=1}^N J_0(qr_{ml}\right\rangle
 
         with :math:`r_{ml}=|\vec{r}_m-\vec{r}_l|` and the Bessel function
-        of the first kind $J_0(x)$.
+        of the first kind :math:`J_0(x)`.
         See also Ref. [1]_ for further information on the
         static structure factor.
 
@@ -1715,7 +1715,7 @@ def __init__(
         .. math::
             C_{\vec{k}_0}(r) = <\exp(i\vec{k}_0\cdot (\vec{r}_j-\vec{r}_l))>
 
-        with $r=|\vec{r}_j-\vec{r}_l|$ (see Ref. [1]_ for further information).
+        with :math:`r=|\vec{r}_j-\vec{r}_l|` (see Ref. [1]_ for further information).
         As shown in Ref. [2]_, this can be rewritten as
 
         .. math::

diff --git a/amep/order.py b/amep/order.py
@@ -1378,8 +1378,8 @@ def psi_k(
         \Psi_k(\vec{r}_j) = \frac{1}{k} \sum_{n=1}^k\exp(ik\theta_{jn}),
 
     where the sum goes over the k nearest neighbors of the particle at
-    position $\vec{r}_j$. The value of $\theta_{jn}$ is equal to the angle
-    between the connection line from $\vec{r}_j$ to $\vec{r}_n$ and the
+    position :math:`\vec{r}_j`. The value of :math:`\theta_{jn}` is equal to the angle
+    between the connection line from :math:`\vec{r}_j` to :math:`\vec{r}_n` and the
     x axis. See also Refs. [1]_ [2]_ [3]_ for further information.
 
     References:

diff --git a/amep/plot.py b/amep/plot.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # =============================================================================
-# Copyright (C) 2023-2024 Lukas Hecht and the AMEP development team.
+# Copyright (C) 2023-2025 Lukas Hecht and the AMEP development team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -45,7 +45,7 @@
 from scipy.spatial import Voronoi, voronoi_plot_2d
 from matplotlib.ticker import MultipleLocator
 from matplotlib.ticker import NullFormatter
-from matplotlib.patches import Rectangle, FancyBboxPatch, ConnectionPatch, Circle
+from matplotlib.patches import Rectangle, FancyBboxPatch, ConnectionPatch, Circle, FancyArrow
 from matplotlib.collections import LineCollection, PatchCollection
 from matplotlib.colors import to_rgba, ListedColormap
 from matplotlib.animation import FuncAnimation
@@ -1885,3 +1885,56 @@ def voronoi(axs: mpl.axes.Axes, vor: Voronoi, **kwargs):
     else:
         raise Exception("amep.plot.voronoi: Cannot plot 3d data.")
     plt.show()
+
+def draw_arrow(fig, x: float, y: float, dx: float, dy: float, **kwargs):
+    r"""Draws an arrow on a Matplotlib figure.
+
+    This function uses the `FancyArrow` class to draw an arrow on a Matplotlib 
+    figure at a specified position, with a given displacement. The arrow is 
+    added directly to the figure object.
+
+    Parameters
+    ----------
+    fig : matplotlib.figure.Figure
+        The Matplotlib figure object on which the arrow will be drawn.
+    x : float
+        The starting x-coordinate of the arrow, in figure coordinates (0 to 1).
+    y : float
+        The starting y-coordinate of the arrow, in figure coordinates (0 to 1).
+    dx : float
+        The horizontal displacement (change in x) of the arrow, in figure coordinates.
+    dy : float
+        The vertical displacement (change in y) of the arrow, in figure coordinates.
+    **kwargs
+        Additional keyword arguments passed to `matplotlib.patches.FancyArrow`, 
+        such as `color`, `width`, `head_width`, and `head_length`.
+
+    Returns
+    -------
+    None.
+
+    Notes
+    -----
+    The arrow's position and size are specified in figure coordinates. Figure 
+    coordinates range from 0 to 1, where (0, 0) represents the bottom-left 
+    corner and (1, 1) represents the top-right corner of the figure.
+
+    Examples
+    --------
+    >>> fig, axs = amep.plot.new(figsize=(3, 3))
+    >>> x=0.2
+    >>> y=0.2
+    >>> dx=0.5
+    >>> dy=0.5
+    >>> amep.plot.draw_arrow(
+    ...     fig, x, y, dx, dy, color="blue", alpha=0.8, width=0.05,
+    ...     head_width=0.1, head_length=0.03
+    ... )
+    >>> 
+
+    """
+    arrow = FancyArrow(
+        x, y, dx, dy, transform=fig.transFigure,
+        length_includes_head=True, **kwargs
+    )
+    fig.add_artist(arrow) 
diff --git a/amep/spatialcor.py b/amep/spatialcor.py
@@ -156,7 +156,7 @@ def spatialcor(
     The spatial correlation function is defined by the following equation
     in which f can be a complex-valued scalar or vector:
 
-    ..math::
+    .. math::
                 C(r) = <f(r)*f(0)> / <f(0)^2>.
 
     Parameters
@@ -1379,7 +1379,11 @@ def sfiso(
     where :math:`N` is the number of particles [1]_.
 
     Mode 'fft' only works in 2D!!!
-
+
+    The minimum wave vector is fixed to :math:`2\pi/L`, where :math:`L` is the
+    box length.
+
+
     References
     ----------
 
@@ -1635,7 +1639,7 @@ def sf2d(
         S(\vec{q}) = \frac{1}{N} \left\langle\sum_{j=1}^{N}\sum_{k=1}^{N}\exp\left\lbrace-i\vec{q}\cdot(\vec{r}_j-\vec{r}_k)\right\rbrace\right\rangle\\
                    = \frac{1}{N} \left\langle\sum_{j=1}^{N}\left\lvert\exp\left\lbrace-i\vec{q}\cdot\vec{r}_j\right\rbrace\right\rvert^2\right\rangle,
 
-    where $\rho(\vec{q})$ is the Fourier transform of the particle number
+    where :math:`\rho(\vec{q})` is the Fourier transform of the particle number
     density (see Ref. [1]_ for further information).

     S(0,0) is set to 0

diff --git a/amep/timecor.py b/amep/timecor.py
@@ -104,7 +104,7 @@ def isf(start, frame, k):
 
         F_{\text{s}}(k,t)=\frac{1}{N}\left\langle\sum_{j=1}^{N}\frac{\sin\left(k\cdot\left|\vec{r}_j\left(t_0+t\right)-\vec{r}_j\left(t_0\right)\right|\right)}{k\cdot\left|\vec{r}_j\left(t_0+t\right)-\vec{r}_j\left(t_0\right)\right|}\right\rangle_{t_0}.
 
-    that can be obtained via taking the mean over all directions of $\vec{k}$.
+    that can be obtained via taking the mean over all directions of :math:`\vec{k}`.
     A detailed derivation can be found in Ref. [1]_.
 
     References

diff --git a/amep/utils.py b/amep/utils.py
@@ -1313,7 +1313,8 @@ def domain_length(
 
         L(t) = 2\pi\frac{\int_{q_{\rm min}}^{q_{\rm max}}{\rm d}q\,S(q,t)}{\int_{q_{\rm min}}^{q_{\rm max}}{\rm d}q\,qS(q,t)}
 
-    and has been used in Refs. [1]_ [2]_ [3]_ [4]_ for example.
+    where :math:`q=n \frac{2\pi}{L}` with :math:`n\in \mathbb{N}` and box legth :math:`L`.
+    It has been used in Refs. [1]_ [2]_ [3]_ [4]_ for example.
 
     References
     ----------
@@ -1356,6 +1357,7 @@ def domain_length(
     l: float
         Domain length as inverse expectation value of q.
 
+
     Examples
     --------
     >>> import amep

diff --git a/test/test_plot.py b/test/test_plot.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # =============================================================================
-# Copyright (C) 2023-2024 Lukas Hecht and the AMEP development team.
+# Copyright (C) 2023-2025 Lukas Hecht and the AMEP development team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -69,6 +69,20 @@ def test_set_locators(self):
         plot.set_locators(axe)
         fig.savefig(PLOT_DIR/"test_locators.pdf")
         close(fig2)
+
+    def test_draw_arrow(self):
+        """Test the amep.plot.draw_arrow method"""
+        fig, axs = plot.new(figsize=(3,3))
+        x = 0.2
+        y = 0.2
+        dx = 0.5
+        dy = 0.5
+        plot.draw_arrow(
+            fig, x, y, dx, dy, color="blue", alpha=0.8, width=0.05,
+            head_width=0.1, head_length=0.03
+        )
+        fig.savefig(PLOT_DIR/"test_draw_arrow.pdf")
+        close(fig)
 
     def test_format_axis(self):
         """Testing the format axis function"""