Removed further references to pybca.

Author: Jon Drobny

examples/benchmark_eam.py

@@ -1,4 +1,4 @@
-from libRustBCA.pybca import *
+from libRustBCA import *
 import numpy as np
 import matplotlib.pyplot as plt
 import sys

examples/benchmark_nnp.py

@@ -0,0 +1,132 @@
+from libRustBCA import *
+import numpy as np
+import matplotlib.pyplot as plt
+import sys
+import os
+#This should allow the script to find materials and formulas from anywhere
+sys.path.append(os.path.dirname(__file__)+'/../scripts')
+sys.path.append('scripts')
+from materials import *
+from formulas import *
+
+R_T_Be = np.array(
+    [
+    [9.67742,	0.016754618],
+    [20.32258,	0.09511873],
+    [30.0,	0.13153034],
+    [49.677418,	0.102242745],
+    [74.83871,	0.08403694],
+    [100.32258,	0.031002639],
+    ]
+)
+
+R_D_Be = np.array(
+    [
+    [10.32258,	0.11649077],
+    [20.32258,	0.19168866],
+    [30.32258,	0.19722955],
+    [49.677418,	0.17269129],
+    [75.16129,	0.11174142],
+    [100.0,	0.044459105],
+    ]
+)
+
+R_H_Be = np.array(
+    [
+    [9.67742,	0.19485489],
+    [19.67742,	0.32150397],
+    [30.0,	0.33575198],
+    [50.322582,	0.25105542],
+    [75.16129,	0.1378628],
+    [100.645164,	0.044459105],
+    ]
+)
+
+#Plotting the MD data points.
+energies = R_H_Be[:, 0]
+R = R_H_Be[:, 1]
+plt.plot(energies, R, marker='o', linestyle='', label='H on Be MD+NNP')
+
+#Plotting the MD data points.
+energies = R_D_Be[:, 0]
+R = R_D_Be[:, 1]
+plt.plot(energies, R, marker='x', linestyle='', label='D on Be MD+NNP')
+
+#Plotting the MD data points.
+energies = R_T_Be[:, 0]
+R = R_T_Be[:, 1]
+plt.plot(energies, R, marker='^', linestyle='', label='T on Be MD+NNP')
+
+
+for ion in [hydrogen, deuterium, tritium]:
+    energies = np.logspace(1, 2, 25)
+    r_rustbca = [reflection_coefficient(ion, beryllium, energy, 0.0, 10000)[0] for energy in energies]
+    r_thomas = [thomas_reflection(ion, beryllium, energy) for energy in energies]
+    line = plt.plot(energies, r_rustbca, label=f'{ion["symbol"]} on Be RustBCA')[0]
+    plt.plot(energies, r_thomas, label=f'{ion["symbol"]} on Be Thomas', linestyle='--', color=line.get_color())
+
+plt.xlabel('E [eV]')
+plt.ylabel('R_N')
+plt.title('Reflection Coefficients')
+plt.legend()
+plt.savefig('reflection_md_nnp_rustbca.png')
+
+#Data digitized from https://doi.org/10.1088/1741-4326/ac592a
+#MD+NNP Sputtering Yields
+y_H_Be = np.array([
+    [20.004726, 0.0029361406],
+    [29.880848, 0.013341782],
+    [49.791046, 0.024575423],
+    [75.00529,	0.016207783],
+    [99.68844,	0.017530797],
+])
+
+y_D_Be = np.array([
+    [19.9699, 0.005002439],
+    [29.601622, 0.021064475],
+    [49.76866,	0.03461476],
+    [74.71549,	0.030082114],
+    [99.954605, 0.013559438],
+])
+
+y_T_Be = np.array([
+    [20.013433, 0.0025699555],
+    [29.85846,	0.01879205],
+    [49.756844, 0.04147379],
+    [74.707405, 0.034042966],
+    [99.68098, 0.01965117],
+])
+
+
+plt.figure()
+
+#Plotting the MD data points.
+energies = y_H_Be[:, 0]
+y = y_H_Be[:, 1]
+plt.semilogy(energies, y, marker='o', linestyle='', label='H on Be MD+NNP')
+
+#Plotting the MD data points.
+energies = y_D_Be[:, 0]
+y = y_D_Be[:, 1]
+plt.semilogy(energies, y, marker='x', linestyle='', label='D on Be MD+NNP')
+
+#Plotting the MD data points.
+energies = y_T_Be[:, 0]
+y = y_T_Be[:, 1]
+plt.semilogy(energies, y, marker='^', linestyle='', label='T on Be MD+NNP')
+
+for ion in [hydrogen, deuterium, tritium]:
+    energies = np.logspace(1, 2, 25)
+    y_rustbca = [sputtering_yield(ion, beryllium, energy, 0.0, 100000) for energy in energies]
+    plt.semilogy(energies, y_rustbca, label=f'{ion["symbol"]} on Be RustBCA')
+
+yamamura_yield = [yamamura(hydrogen, beryllium, energy) for energy in energies]
+plt.semilogy(energies, yamamura_yield, label='Yamamura H on Be', linestyle='--')
+
+plt.title('Sputtering Yields of Hydrogenic Species on Be')
+plt.xlabel('E [eV]')
+plt.ylabel('Y [at/ion]')
+plt.gca().set_ylim([1e-4, 1e-1])
+plt.legend(loc='lower right')
+
+plt.savefig('sputtering_md_nnp_rustbca.png')

examples/test_morse.py

@@ -1,4 +1,4 @@
-from libRustBCA.pybca import *
+from libRustBCA import *
 import numpy as np
 import matplotlib.pyplot as plt
 import sys