added crystal generater

cal.py

@@ -0,0 +1,62 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+
+def deg_2_rad(winkel):
+    return winkel/180.0 * np.pi
+
+
+# all units in angstrom
+base_a_m = 5.75
+base_b_m = 4.5
+base_c_m = 5.38
+
+base_c_r = 2.856
+base_b_r = 4.554
+base_a_r = base_b_r
+
+alpha_m = 122.64  # degree
+
+
+def mono_2_rutile(c_m, a_m):
+    a_r = np.cos(deg_2_rad(alpha_m - 90)) * c_m * base_c_m
+    c_r = (a_m) * base_a_m + np.sin(deg_2_rad(alpha_m - 90)) * c_m * base_c_m
+    return a_r, c_r
+
+
+def main():
+    offset_a_m = 0.25 - 0.23947
+    offset_c_m = 0.02646
+
+    offset_a_r, offset_c_r = mono_2_rutile(offset_c_m, offset_a_m)
+
+    print("A_r: ", offset_a_r, "C_r: ", offset_c_r)
+
+    x = np.arange(10)
+    y = np.arange(10)
+    X, Y = np.meshgrid(x, y)
+
+    atom_x = offset_a_r + X * base_c_r + np.mod(Y, 4) * 0.5 * base_c_r
+    atom_x[np.mod(X, 2) == 0] -= 2 * offset_a_r
+
+    atom_y = offset_c_r + 0.5 * Y * base_a_r
+    atom_y[np.mod(X, 2) == 0] -= 2 * offset_c_r
+
+    fig, ax = plt.subplots(1)
+    plt.scatter(atom_x, atom_y)
+
+    atom_x_rut = X * base_c_r + np.mod(Y, 4) * 0.5 * base_c_r
+    atom_y_rut = Y * 0.5 * base_a_r
+
+    plt.scatter(atom_x_rut, atom_y_rut)
+    print(np.square(atom_x-atom_x_rut) + np.square(atom_y-atom_y_rut))
+
+    cryst = np.loadtxt("./crystal_V.xyz", delimiter=" ")
+    print(cryst.shape)
+    plt.scatter(-cryst[:, 0]+5.5*base_c_r, cryst[:, 2])
+    ax.set_aspect(1)
+    plt.show()
+
+
+if __name__ == "__main__":
+    main()

crystal_V.xyz

@@ -0,0 +1,24 @@
+-1.317409 0.112925 -0.113205
+-1.317410 4.629925 -0.113205
+9.907514 -0.112924 4.641385
+9.907513 4.404076 4.641385
+1.317409 -0.112925 0.113205
+-1.578486 -0.112924 4.641385
+4.425591 0.112925 -0.113205
+4.425590 4.629925 -0.113205
+7.060409 -0.112925 0.113205
+4.164514 -0.112924 4.641385
+10.168591 0.112925 -0.113205
+10.168590 4.629925 -0.113205
+1.317408 4.404075 0.113205
+2.977644 2.145576 2.150886
+1.529697 0.112926 4.414976
+-0.130539 2.371426 2.377295
+-1.578487 4.404076 4.641385
+1.529696 4.629926 4.414976
+7.060408 4.404075 0.113205
+8.720644 2.145576 2.150886
+7.272697 0.112926 4.414976
+5.612461 2.371426 2.377295
+4.164513 4.404076 4.641385
+7.272696 4.629926 4.414976

crystal_maker.xyz

@@ -0,0 +1,42 @@
+V -1.317409 0.112925 -0.113205
+O -1.443069 3.207070 1.358454
+O -2.891016 3.568431 3.622545
+V -1.317410 4.629925 -0.113205
+V 9.907514 -0.112924 4.641385
+O 11.481121 0.948570 0.905636
+O 10.033174 1.309931 3.169726
+V 9.907513 4.404076 4.641385
+V 1.317409 -0.112925 0.113205
+V -1.578486 -0.112924 4.641385
+V 4.425591 0.112925 -0.113205
+V 4.425590 4.629925 -0.113205
+V 7.060409 -0.112925 0.113205
+V 4.164514 -0.112924 4.641385
+V 10.168591 0.112925 -0.113205
+V 10.168590 4.629925 -0.113205
+O -0.004879 0.948570 0.905636
+O 4.299931 3.207070 1.358454
+O 2.851984 3.568431 3.622545
+O 1.399960 3.116730 1.313172
+O 2.895092 0.858230 0.950918
+O 1.447145 1.400271 3.215008
+O -0.047988 3.658771 3.577263
+V 1.317408 4.404075 0.113205
+V 2.977644 2.145576 2.150886
+V 1.529697 0.112926 4.414976
+V -0.130539 2.371426 2.377295
+V -1.578487 4.404076 4.641385
+V 1.529696 4.629926 4.414976
+O 5.738121 0.948570 0.905636
+O 8.594984 3.568431 3.622545
+O 4.290174 1.309931 3.169726
+O 7.142960 3.116730 1.313172
+O 8.638092 0.858230 0.950918
+O 7.190145 1.400271 3.215008
+O 5.695012 3.658771 3.577263
+V 7.060408 4.404075 0.113205
+V 8.720644 2.145576 2.150886
+V 7.272697 0.112926 4.414976
+V 5.612461 2.371426 2.377295
+V 4.164513 4.404076 4.641385
+V 7.272696 4.629926 4.414976