made pip installable

PyCrystallography/PyShapes.py

@@ -0,0 +1,281 @@
+import numpy as np
+from PyCrystallography import plot_axis,make_atom,make_bond,plot_bonds,plot_atoms
+
+def normal_points(ax,faces,r):
+    """
+    """
+
+    sphere_points = []
+
+    for face in faces:
+
+        points_sum = np.array([0,0,0])
+
+        for vert in face:
+            points_sum = points_sum + vert
+
+        face_centre = points_sum/len(face)
+
+
+        vert1 = face[0]
+        vert2 = face[1]
+        vert3 = face[2]
+
+        vec1 = [vert2[0]-vert1[0],vert2[1]-vert1[1],vert2[2]-vert1[2]]
+        vec2 = [vert3[0]-vert1[0],vert3[1]-vert1[1],vert3[2]-vert1[2]]
+
+        normal = np.cross(vec1,vec2)
+      #  print(normal)
+
+        # generate projected point on a sphere of radius r
+        normal = face_centre+normal
+
+        # scale to be on sphere
+        current_r = np.sqrt(normal[0]**2 + normal[1]**2 + normal[2]**2)
+
+        normal = normal * r/current_r
+
+        current_r = np.sqrt(normal[0]**2 + normal[1]**2 + normal[2]**2)
+       # print(current_r)
+
+        if normal[2] > 0:
+            COL ='blue'
+        elif normal[2] == 0:
+            COL ='green'
+        else:
+            COL='r'
+
+        sphere_points.append(normal)
+        ax.plot([face_centre[0],normal[0]],[face_centre[1],normal[1]],[face_centre[2],normal[2]],linewidth=3,c='k')
+        ax.scatter(normal[0],normal[1],normal[2],linewidth=3,c=COL)
+
+    return sphere_points
+
+def plot_face(ax,verts,alpha=0.5,color='C0'):
+    """
+    """
+
+    x_list = []
+    y_list = []
+    z_list = []
+
+    for vert in verts:
+        x_list.append(vert[0])
+        y_list.append(vert[1])
+        z_list.append(vert[2])
+
+    verts = [list(zip(x_list,y_list,z_list))]
+
+    from mpl_toolkits.mplot3d.art3d import Poly3DCollection
+    ax.add_collection3d(Poly3DCollection(verts,linewidths=1,edgecolor='k',alpha=alpha,color=color))
+
+def cuboid(ax,h,w,d,alpha=0.5,show_axis=True):
+    """
+    """
+    if show_axis == True:
+        plot_axis(ax,max_lim=1.5*max(h,w,d))
+    faces = []
+
+    #+w
+    side_verts1 = [h/2,w/2,-d/2],[-h/2,w/2,-d/2],[-h/2,w/2,d/2],[h/2,w/2,d/2]
+    faces.append(side_verts1)
+
+    #-w
+    side_verts2 = [h/2,-w/2,d/2],[-h/2,-w/2,d/2],[-h/2,-w/2,-d/2],[h/2,-w/2,-d/2]
+
+    faces.append(side_verts2)
+
+    #+h
+    side_verts3 = [h/2,w/2,d/2],[h/2,-w/2,d/2],[h/2,-w/2,-d/2],[h/2,w/2,-d/2]
+    faces.append(side_verts3)
+
+    #-h
+    side_verts4 = [-h/2,w/2,-d/2],[-h/2,-w/2,-d/2],[-h/2,-w/2,d/2],[-h/2,w/2,d/2]
+    faces.append(side_verts4)
+
+    #+d
+    top_verts = [h/2,w/2,d/2],[-h/2,w/2,d/2],[-h/2,-w/2,d/2],[h/2,-w/2,d/2]
+    faces.append(top_verts)
+
+    #-d
+    bottom_verts = [h/2,-w/2,-d/2],[-h/2,-w/2,-d/2],[-h/2,w/2,-d/2],[h/2,w/2,-d/2]
+
+    faces.append(bottom_verts)
+
+    for face in faces:
+        plot_face(ax,face,alpha=alpha)
+
+    return faces
+
+
+def prism(ax,h_z,r_xy,num_of_side):
+    """
+    will plot a prism of given height, width and depth in x,y, and z
+    """
+    h = h_z
+    r = r_xy
+
+    plot_axis(ax,max_lim=1.5*max(h_z,r_xy))
+
+    faces = []
+
+    top_verts    = []
+    bottom_verts = []
+
+    for n in range(0,num_of_side):
+        theta      = (2*n/num_of_side)*np.pi + np.pi/4
+        theta_next = (2*(n+1)/num_of_side)*np.pi+ np.pi/4
+
+        x = (r)*np.cos(theta)
+        y = (r)*np.sin(theta)
+
+        x_next = (r)*np.cos(theta_next)
+        y_next = (r)*np.sin(theta_next)
+
+        side_verts = [x,y,-h/2],[x_next,y_next,-h/2],[x_next,y_next,h/2],[x,y,h/2]
+        faces.append(side_verts)
+
+        top_verts.append([x,y,h/2])
+        bottom_verts.append([x,y,-h/2])
+
+    faces.append(top_verts)
+    faces.append(bottom_verts[::-1])
+
+    for face in faces:
+        plot_face(ax,face)
+
+    return faces
+
+def tetrakis(ax,r,dr):
+    """
+    will plot a tetrakis
+    """
+    faces = []
+
+    top_verts    = []
+    bottom_verts = []
+
+    plot_axis(ax,max_lim=1.1*(r+2*dr))
+    for n in range(0,4):
+        theta      = (2*n/4)*np.pi + np.pi/4
+        theta_next = (2*(n+1)/4)*np.pi+ np.pi/4
+        theta_mid  = (2*(n+0.5)/4)*np.pi+ np.pi/4
+
+        x = (r)*np.cos(theta)
+        y = (r)*np.sin(theta)
+
+        x_mid = (r+dr)*np.cos(theta_mid)
+        y_mid = (r+dr)*np.sin(theta_mid)
+        z_mid = 0
+
+        x_next = (r)*np.cos(theta_next)
+        y_next = (r)*np.sin(theta_next)
+
+        h = 2*r*np.sin(np.pi/4)
+
+        side_verts_top = [0,0,h/2+dr],[x,y,h/2],[x_next,y_next,h/2]
+        faces.append(side_verts_top)
+
+        side_verts_mid_up = [x_mid,y_mid,z_mid],[x_next,y_next,h/2],[x,y,h/2]
+
+        faces.append(side_verts_mid_up)
+
+        side_verts_mid_left = [x_mid,y_mid,z_mid],[x,y,h/2],[x,y,-h/2]
+        faces.append(side_verts_mid_left)
+
+        side_verts_mid_right = [x_next,y_next,-h/2],[x_next,y_next,h/2],[x_mid,y_mid,z_mid]
+        faces.append(side_verts_mid_right)
+
+        side_verts_mid_down = [x,y,-h/2],[x_next,y_next,-h/2],[x_mid,y_mid,z_mid]
+        faces.append(side_verts_mid_down)
+
+        side_verts_bottom = [x_next,y_next,-h/2],[x,y,-h/2],[0,0,-h/2-dr]
+        faces.append(side_verts_bottom)
+
+    for face in faces:
+        plot_face(ax,face)
+
+    return faces
+
+def pyramid(ax,h,r,num_of_side):
+    """
+    will plot a pyramid with num of sides -1
+    """
+    faces = []
+    bottom_verts = []
+    plot_axis(ax,max_lim=1.1*h)
+
+    for n in range(0,num_of_side):
+        theta      = (2*n/num_of_side)*np.pi
+        theta_next = (2*(n+1)/num_of_side)*np.pi
+        x = r*np.cos(theta)
+        y = r*np.sin(theta)
+
+        x_next = r*np.cos(theta_next)
+        y_next = r*np.sin(theta_next)
+
+        side_verts = [0,0,h/2],[x,y,-h/2],[x_next,y_next,-h/2]
+        faces.append(side_verts)
+        bottom_verts.append([x,y,-h/2])
+
+    faces.append(bottom_verts[::-1])
+
+    for face in faces:
+        plot_face(ax,face)
+
+    return faces
+
+def bipyramid(ax,h,r,num_of_side):
+    """
+    will plot a bipyramid with number of sides /2
+    """
+    faces = []
+    plot_axis(ax,max_lim=1.1*max(h,r))
+    for n in range(0,num_of_side):
+        theta      = (2*n/num_of_side)*np.pi
+        theta_next = (2*(n+1)/num_of_side)*np.pi
+        x = r*np.cos(theta)
+        y = r*np.sin(theta)
+
+        x_next = r*np.cos(theta_next)
+        y_next = r*np.sin(theta_next)
+
+        side_verts_top = [0,0,h/2],[x,y,0],[x_next,y_next,0]
+        faces.append(side_verts_top)
+
+        side_verts_bottom = [x_next,y_next,0],[x,y,0],[0,0,-h/2]
+        faces.append(side_verts_bottom)
+
+    for face in faces:
+        plot_face(ax,face)
+
+    return faces
+
+def biprismid(ax,h,dh,r,num_of_side):
+    """
+    will plot a bi-prism-id with number of sides /2
+    """
+    faces = []
+    plot_axis(ax,max_lim=1.1*max(h,r))
+    for n in range(0,num_of_side):
+        theta      = (2*n/num_of_side)*np.pi
+        theta_next = (2*(n+1)/num_of_side)*np.pi
+        x = r*np.cos(theta)
+        y = r*np.sin(theta)
+
+        x_next = r*np.cos(theta_next)
+        y_next = r*np.sin(theta_next)
+
+        side_verts_top = [0,0,h/2+dh],[x,y,h/2],[x_next,y_next,h/2]
+        faces.append(side_verts_top)
+
+        side_verts_mid = [x,y,-h/2],[x_next,y_next,-h/2],[x_next,y_next,h/2],[x,y,h/2]
+        faces.append(side_verts_mid)
+
+        side_verts_bottom = [x_next,y_next,-h/2],[x,y,-h/2],[0,0,-h/2-dh]
+        faces.append(side_verts_bottom)
+
+    for face in faces:
+        plot_face(ax,face)
+
+    return faces

PyCrystallography/main.py

@@ -0,0 +1,21 @@
+import matplotlib
+matplotlib.use('TkAgg')
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+from PyShapes import *
+from PyCrystallography import *
+
+fig = plt.figure(0,figsize=[8,8])
+ax = fig.add_subplot(111,projection='3d')
+#faces = cuboid(ax,2,2,2)
+#reflection(ax,2,2,2)
+faces=pyramid(ax,2,2,3)
+# faces=biprismid(ax,3,1,0.5,5)
+points=normal_points(ax,faces,5)
+# print(points)
+
+# ns,es,ss=Stereographic_projection(points,3,'test')
+# #print(ns,ss)
+# identify_fold_symmetry(ns,es,ss)
+plt.show()

PyCrystallography/test.py

@@ -0,0 +1,7 @@
+import matplotlib.pyplot as plt
+fig = plt.figure(0,figsize=[8,8])
+azim = 30
+ax = fig.add_subplot(111,projection='3d',azim=azim,elev=30)
+from PyCrystallography import reflection
+reflection(ax,1,1,1)
+plt.show()

setup.py

@@ -0,0 +1,27 @@
+from setuptools import setup, find_packages
+
+# with open("README.md", "r") as f:
+#     README = f.read()
+
+setup(
+    name='PyCrystallography',
+    version='0.1.1',
+    description='Python 3 package being written to illustrate crystallography',
+    long_description='Python 3 package being written to illustrate crystallography', # fix readme import
+    long_description_content_type='text/markdown',
+    author='Shellywell123',
+    url='https://github.com/Shellywell123/PyCrystallography',
+    packages=find_packages(),
+    install_requires=[
+        'matplotlib>=3.3.2',
+        'numpy>=1.19.2',
+        'imageio>=2.9.0'
+    ],
+    python_requires='>=3.6',
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    ],
+    zip_safe=False
+)