SAMBA-ilum 1.0.0.409__tar.gz → 1.0.0.411__tar.gz

{samba_ilum-1.0.0.409 → samba_ilum-1.0.0.411}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.409
+Version: 1.0.0.411
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.409 → samba_ilum-1.0.0.411}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.409
+Version: 1.0.0.411
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.409 → samba_ilum-1.0.0.411}/SAMBA_ilum.egg-info/SOURCES.txt

@@ -33,6 +33,7 @@ samba_ilum/src/potcar.py
 samba_ilum/src/vdW_DF.py
 samba_ilum/src/xy-scan.py
 samba_ilum/src/xy-scan_analysis.py
+samba_ilum/src/xy-scan_analysis_old.py
 samba_ilum/src/xyz-scan.py
 samba_ilum/src/xyz-scan_analysis.py
 samba_ilum/src/z-scan.py

{samba_ilum-1.0.0.409 → samba_ilum-1.0.0.411}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.409'
+version = '1.0.0.411'
 
 print(" ")
 print("=============================================================")

{samba_ilum-1.0.0.409 → samba_ilum-1.0.0.411}/samba_ilum/src/make_files.py

@@ -270,7 +270,7 @@ for i in range(len(files)):
            # Atualizando o arquivo input.vasprocar.location --------------------------------------------
            #--------------------------------------------------------------------------------------------
            with open(dir_task + '/inputs/input.vasprocar.location', "r") as file:  content = file.read()
-           content = content.replace('replace_n_reg', str(n_materials))
+           content = content.replace('replace_n_reg', str(len(label_materials)))
            for m in range(len(label_materials)):
                content = content.replace('replace_label_Lattice' + str(m+1), str(label_materials[m].replace('_', '')))
                content = content.replace('replace_nion_Lattice' + str(m+1), str(range_ion_Lattice[m]))

samba_ilum-1.0.0.411/samba_ilum/src/xy-scan_analysis.py

@@ -0,0 +1,265 @@
+# SAMBA_ilum Copyright (C) 2024 - Closed source
+
+
+# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+# Observação:  Introduzir o vácuo original no arquivo POSCAR final
+# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+import numpy as np
+import shutil
+import os
+#--------------------------
+import plotly.offline as py
+import plotly.graph_objects as go
+#--------------------------------
+import scipy.interpolate as interp
+from scipy.interpolate import griddata
+#-------------------------------------
+import matplotlib as mpl
+from matplotlib import cm
+from matplotlib import pyplot as plt
+import matplotlib.ticker as ticker
+from mpl_toolkits.mplot3d.axes3d import Axes3D
+from matplotlib.ticker import LinearLocator, FormatStrFormatter
+import matplotlib.colors as mcolors
+
+
+n_d = 301  # O dados do xy-scan serão interpolados para um grid de (n_d x n_d) pontos
+
+
+#========================================================
+# Obtendo a área no plano XY da Heteroestrutura =========
+#========================================================
+poscar = open('POSCAR.0', 'r')
+VTemp = poscar.readline().split()
+VTemp = poscar.readline();  param = float(VTemp)
+#-----------------------------------------------
+A1 = poscar.readline().split();  A1x = float(A1[0])*param; A1y = float(A1[1])*param; A1z = float(A1[2])*param;  mA1 = np.linalg.norm(A1)
+A2 = poscar.readline().split();  A2x = float(A2[0])*param; A2y = float(A2[1])*param; A2z = float(A2[2])*param;  mA2 = np.linalg.norm(A2)
+A3 = poscar.readline().split();  A3x = float(A3[0])*param; A3y = float(A3[1])*param; A3z = float(A3[2])*param;  mA3 = np.linalg.norm(A3)
+#---------------------------------------------------------------------------------------------------------------------------------------
+A1 = np.array([A1x, A1y])
+A2 = np.array([A2x, A2y])
+#---------------------------
+# Área da célula no plano XY
+Area = np.linalg.norm(np.cross(A1, A2))
+#--------------------------------------
+poscar.close()
+#-------------
+
+
+#=====================================================
+# Extraindo informações do arquivo energy_scan.txt ===
+#=====================================================
+file0 = np.loadtxt('energy_scan.txt', dtype=str)
+file0.shape
+#-----------------------
+date_shift  = file0[:,0]
+date_E   = np.array(file0[:,1],dtype=float)
+E_min    = min(date_E)
+E_max    = max(date_E)
+Delta_E_meV = ((E_max -E_min)*1000)/Area
+Delta_E_J   = ((E_max -E_min)*1.6021773e-19)/(Area*1e-20)
+line     = np.argmin(date_E)
+delta    = date_shift[line]
+#------------------------------------------
+delta_min = delta.replace('_', ' ').split()
+a1_min = float(delta_min[0])
+a2_min = float(delta_min[1])
+x_min = (a1_min*A1x) + (a2_min*A2x)
+y_min = (a1_min*A1y) + (a2_min*A2y)
+#----------------------------------
+if (a1_min == -0.0): a1_min = 0.0
+if (a2_min == -0.0): a2_min = 0.0
+if (x_min == -0.0):  x_min = 0.0
+if (y_min == -0.0):  y_min = 0.0
+#-------------------------------
+
+
+#===============================================
+# Criando o arquivo energy_scan_shift.txt ======
+#===============================================
+file0 = np.loadtxt('energy_scan.txt', dtype=str)
+file0.shape
+#----------------------
+date_shift = file0[:,0]
+date_E = np.array(file0[:,1],dtype=float)
+#----------------------------------------
+file = open('energy_scan_shift.txt', "w")
+shift = [-2, -1, 0, +1, +2]
+#-------------------------------
+for i in range(len(date_shift)):
+    #--------------------------------------------------
+    shift_temp = date_shift[i].replace('_',' ').split()
+    shift_A1 = float(shift_temp[0])
+    shift_A2 = float(shift_temp[1])
+    #------------------------------
+    for j in range(len(shift)):
+        for k in range(len(shift)):
+            t_shift_A1 = shift_A1 -a1_min +shift[j]
+            t_shift_A2 = shift_A2 -a2_min +shift[k]
+            if (t_shift_A1 >= 0.0  and t_shift_A1 <= 1.0):
+               if (t_shift_A2 >= 0.0  and t_shift_A2 <= 1.0): 
+                  file.write(f'{shift_A1 -a1_min +shift[j]}_{shift_A2 -a2_min + shift[k]} {date_E[i]} \n')
+#-----------
+file.close()
+#-----------
+
+
+#===========================================================
+# Extraindo informações do arquivo energy_scan_shift.txt ===
+#===========================================================
+file0 = np.loadtxt('energy_scan_shift.txt', dtype=str)
+file0.shape
+#----------------------
+date_shift = file0[:,0]
+date_E = np.array(file0[:,1],dtype=float)
+E_min    = min(date_E)
+#---------------------
+
+
+#-------------------------------------
+file = open('xy-scan_direct.dat', "w")
+#-------------------------------------
+for i in range(len(date_shift)):
+    VTemp = str(date_shift[i])
+    VTemp = VTemp.replace('_', ' ')
+    file.write(f'{VTemp} {((date_E[i] -E_min)*1000)/Area} \n')
+#-----------
+file.close()
+#-----------
+
+
+#----------------------------------------
+file = open('xy-scan_cartesian.dat', "w")
+#----------------------------------------
+for i in range(len(date_shift)):
+    VTemp = str(date_shift[i])
+    VTemp = VTemp.replace('_', ' ').split()
+    Coord_X = ((float(VTemp[0])*A1x) + (float(VTemp[1])*A2x))
+    Coord_Y = ((float(VTemp[0])*A1y) + (float(VTemp[1])*A2y))
+    file.write(f'{Coord_X} {Coord_Y} {((date_E[i] -E_min)*1000)/Area} \n')
+#-----------
+file.close()
+#-----------
+
+
+#===================================================
+# Plot 3D - Coordenadas Cartesianas (.html) ========
+#===================================================
+label1 = '\u0394' + 'X' + ' (' + '\u212B' + ')'
+label2 = '\u0394' + 'Y' + ' (' + '\u212B' + ')'
+label3 = 'E-Emin' + ' (meV/' + '\u212B' + '\u00B2' + ')'
+#------------------------------------------------------------
+file2 = np.loadtxt('xy-scan_cartesian.dat')
+file2.shape
+#------------------
+eixo1c = file2[:,0]
+eixo2c = file2[:,1]
+eixo3c = file2[:,2]
+#---------------------------
+# Create meshgrid for (x, y):
+x = np.linspace(min(eixo1c), max(eixo1c), n_d)
+y = np.linspace(min(eixo2c), max(eixo2c), n_d)
+x_grid, y_grid = np.meshgrid(x, y)
+# Grid data:
+e2_grid = griddata((eixo1c, eixo2c), eixo3c, (x_grid, y_grid), method = 'cubic', fill_value=np.nan)
+
+
+#============================================================
+# Obtendo as coordenadas do ponto de E_mínima ===============
+#============================================================
+e2_grid[np.isnan(e2_grid)] = np.inf
+min_idx = np.unravel_index(np.argmin(e2_grid), e2_grid.shape)   # Encontrando o índice do menor valor de energia no e_grid
+delta_X = x_grid[min_idx]                                       # Encontrando o correspondente valor de delta_X
+delta_Y = y_grid[min_idx]                                       # Encontrando o correspondente valor de delta_Y
+E_min   = e2_grid[min_idx]                                      # Encontrando o correspondente valor de E_min
+# print(min_idx, delta_X, delta_Y, E_min)
+#----------------------------------------
+fig = go.Figure()
+fig.add_trace(go.Surface(x = x_grid, y = y_grid, z = e2_grid, name = 'xy-scan', opacity = 0.8, showscale = False, colorscale='jet'))
+fig.update_layout(title = 'xy-scan', scene = dict(xaxis_title = label1, yaxis_title = label2, zaxis_title = label3, aspectmode = 'cube'), margin = dict(r = 20, b = 10, l = 10, t = 10))
+fig.update_layout(xaxis_range=[min(eixo1c), max(eixo1c)])
+fig.update_layout(yaxis_range=[min(eixo2c), max(eixo2c)])
+fig.write_html('xy-scan_3D_cartesian.html')
+
+
+#===========================================================================
+# Obtendo as coordenadas do ponto de E_mínima na forma direta ==============
+#===========================================================================
+a = np.array([A1x, A1y, A1z])
+b = np.array([A2x, A2y, A2z])
+c = np.array([A3x, A3y, A3z])
+T = np.linalg.inv(np.array([a, b, c]).T)  # Definindo a matriz de transformação
+#------------------------------------------------------------------------------
+r = np.array([delta_X, delta_Y, 0.0])        # Definindo o vetor posição cartesiano do átomo
+#------------------------------------
+f = np.dot(T, r)           # Calculando a correspondenre posição em coordenadas fracionárias    # ??????????????????? Esta correto ???????????????????
+for m in range(3):                                                                              # ?????? Ao invés de 'f' não deveria ser 'f[m]' ??????
+    f = np.where(f < 0, f + 1, f)                                                               # ??????????????????? Esta correto ???????????????????
+    f = np.where(f > 1, f - 1, f)
+#--------------------------------
+for m in range(3):
+    # f[m] = round(f[m], 6)
+    if (f[m] > 0.9999 or f[m] < 0.0001):
+       f[m] = 0.0
+#------------------------------------
+delta_A1 = float(f[0])
+delta_A2 = float(f[1])
+
+
+#=======================================================
+# Plot 2D - Coordenadas Cartesianas (Mapa de cores) ====
+#=======================================================
+n_contour = 100
+#------------------------------------
+mod_x = abs(max(eixo1c) -min(eixo1c))
+mod_y = abs(max(eixo2c) -min(eixo2c))
+#----------------------------------------------------------------
+cmap_gray = (mpl.colors.ListedColormap(['darkgray', 'darkgray']))
+#-----------------------
+fig, ax = plt.subplots()
+cp = plt.contourf(x_grid, y_grid, e2_grid, levels = n_contour, cmap = 'jet', alpha = 1.0, antialiased = True)
+plt.quiver(0, 0, A1x, A1y, angles='xy', scale_units='xy', scale=1, color='black', label='A$_1$')
+plt.quiver(0, 0, A2x, A2y, angles='xy', scale_units='xy', scale=1, color='black', label='A$_2$')
+plt.text((A1x/2), (A1y/2), "A$_1$", fontsize=10, color="black")
+plt.text((A2x/2), (A2y/2), "A$_2$", fontsize=10, color="black")
+# plt.scatter(delta_X, delta_Y, c='black', marker='o', s=2)
+# plt.scatter(x_min, y_min, c='black', marker='o', s=2)
+cbar = fig.colorbar(cp, orientation = 'vertical', shrink = 1.0)
+#-------------------
+plt.title('xy-scan')
+plt.xlabel('$\Delta$X' + '$\ ({\AA})$')
+plt.ylabel('$\Delta$Y' + '$\ ({\AA})$')
+cbar.set_label('$E-E_{min}\ $(meV/${\AA^2})$')
+#---------------------------------------------
+ax.set_box_aspect(mod_y/mod_x)
+#------------------------------------------------------------------------------
+plt.savefig('xy-scan_cartesian.png', dpi = 600, bbox_inches='tight', pad_inches = 0)
+# plt.savefig('xy-scan_cartesian.pdf', dpi = 600, bbox_inches='tight', pad_inches = 0)
+# plt.savefig('xy-scan_cartesian.eps', dpi = 600, bbox_inches='tight', pad_inches = 0)
+# plt.savefig('xy-scan_cartesian.svg', dpi = 600, bbox_inches='tight', pad_inches = 0)
+
+
+#--------------------------------------------------
+shutil.copyfile(str(delta) + '/POSCAR', 'POSCAR')
+shutil.copyfile(str(delta) + '/CONTCAR', 'CONTCAR')
+#----------------------------------------------------
+
+
+#=====================================================
+info = open('info_xy-scan.dat', "w", encoding='utf-8')
+info.write(f'====================================================== \n')
+info.write(f'Displacement carried out over the 2nd material lattice   \n')
+#------------------------------------------------------------------
+info.write(f'Displacement_XY = ({x_min}, {y_min}) in Å \n')
+info.write(f'Displacement_XY = ({a1_min}*A1, {a2_min}*A2) \n')
+#----------------------------------------------------------------
+# info.write(f'Displacement_XY = ({delta_X}, {delta_Y}) in Å \n')
+# info.write(f'Displacement_XY = ({delta_A1}*A1, {delta_A2}*A2) \n')
+info.write(f'------------------------------------------------------ \n')
+info.write(f'ΔE = {Delta_E_meV:.12f} meV/Å^2  or  {Delta_E_J:.12f} J/m^2 \n')
+info.write(f'====================================================== \n')
+info.close()
+#===========

samba_ilum-1.0.0.409/samba_ilum/src/xy-scan_analysis.py → samba_ilum-1.0.0.411/samba_ilum/src/xy-scan_analysis_old.py

@@ -206,7 +206,7 @@ plt.quiver(0, 0, A2x, A2y, angles='xy', scale_units='xy', scale=1, color='black'
 plt.text((A1x/2), (A1y/2), "A$_1$", fontsize=10, color="black")
 plt.text((A2x/2), (A2y/2), "A$_2$", fontsize=10, color="black")
 # plt.scatter(delta_X, delta_Y, c='black', marker='o', s=2)
-plt.scatter(x_min, y_min, c='black', marker='o', s=2)
+# plt.scatter(x_min, y_min, c='black', marker='o', s=2)
 cbar = fig.colorbar(cp, orientation = 'vertical', shrink = 1.0)
 #-------------------
 plt.title('xy-scan')
@@ -271,7 +271,7 @@ cmap_gray = (mpl.colors.ListedColormap(['darkgray', 'darkgray']))
 #-----------------------
 fig, ax = plt.subplots()
 cp = plt.contourf(a1_grid, a2_grid, e1_grid, levels = n_contour, cmap = 'jet', alpha = 1.0, antialiased = True)
-plt.scatter(delta_A1, delta_A2, c='black', marker='o', s=2)
+# plt.scatter(delta_A1, delta_A2, c='black', marker='o', s=2)
 cbar = fig.colorbar(cp, orientation = 'vertical', shrink = 1.0)
 #-------------------
 plt.title('xy-scan')

{samba_ilum-1.0.0.409 → samba_ilum-1.0.0.411}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.409",
+    version = "1.0.0.411",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",