SAMBA-ilum 1.0.0.415__tar.gz → 1.0.0.417__tar.gz

{samba_ilum-1.0.0.415 → samba_ilum-1.0.0.417}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.415
+Version: 1.0.0.417
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.415 → samba_ilum-1.0.0.417}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.415
+Version: 1.0.0.417
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.415 → samba_ilum-1.0.0.417}/SAMBA_ilum.egg-info/SOURCES.txt

@@ -10,6 +10,7 @@ SAMBA_ilum.egg-info/requires.txt
 SAMBA_ilum.egg-info/top_level.txt
 samba_ilum/__init__.py
 samba_ilum/__main__.py
+samba_ilum/src/BZ_2D.py
 samba_ilum/src/HeteroStructure_Generator.py
 samba_ilum/src/_info_pseudo.py
 samba_ilum/src/a-scan.py

{samba_ilum-1.0.0.415 → samba_ilum-1.0.0.417}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.415'
+version = '1.0.0.417'
 
 print(" ")
 print("=============================================================")

samba_ilum-1.0.0.417/samba_ilum/src/BZ_2D.py

@@ -0,0 +1,163 @@
+#-----------------
+import numpy as np
+import os
+#----------------
+import matplotlib
+import matplotlib.colors as mcolors
+import matplotlib.pyplot as plt
+#--------------------------------
+from scipy.spatial import Voronoi
+#--------------------------------
+
+
+
+#============================================================
+# Extraindo o k-path usado no plot da Estrutura de Bandas ===
+#============================================================
+kpoints_file = []
+kpath = []
+#---------
+if os.path.isdir('output/Bandas'):     dir_kpath = 'bands'
+if os.path.isdir('output/Bandas.SO'):  dir_kpath = 'bands.SO'
+#-----------------------------------------------------------------------------
+if os.path.isfile(dir_kpath + '/' + 'KPOINTS'): kpoints_file.append('KPOINTS')
+#--------------------------------------------------------------------------------------
+nkpoints = len([file for file in os.listdir(dir_kpath) if file.startswith("KPOINTS.")])
+for i in range(nkpoints):
+    file = 'KPOINTS.' + str(i+1)
+    if os.path.isfile(dir_kpath + '/' + file): kpoints_file.append(file)
+#---------------------------------
+for i in range(len(kpoints_file)):
+    #-----------------------------
+    with open(dir_kpath + '/' + kpoints_file[i], 'r') as file: lines = file.readlines()
+    #----------------------------------------------------------------------------------
+    if (len(kpoints_file) == 1):
+       for j in range(len(lines)):
+           if (j > 3 and len(lines[j]) > 1):
+              line = lines[j].split()
+              line[3] = line[3].replace('!', '').replace('#1', 'Gamma').replace('#', '')
+              if (line[3] == 'Gamma' or line[3] == 'gamma' or line[3] == 'G' or line[3] == 'g'): line[3] = '${\\Gamma}$'
+              kpath.append([float(line[0]), float(line[1]), float(line[2]), str(line[3])])
+    #-------------------------------------------------------------------------------------
+    if (len(kpoints_file) > 1):
+       for j in range(len(lines)):
+           if (i == 0 and j > 3 and len(lines[j]) > 1):
+              line = lines[j].split()
+              line[3] = line[3].replace('!', '').replace('#1', 'Gamma').replace('#', '')
+              kpath.append([float(line[0]), float(line[1]), float(line[2]), str(line[3])])
+           if (i > 0  and j > 4 and len(lines[j]) > 1):
+              line = lines[j].split()
+              line[3] = line[3].replace('!', '').replace('#1', 'Gamma').replace('#', '')
+              kpath.append([float(line[0]), float(line[1]), float(line[2]), str(line[3])])
+#-----------------------------------------------------------------------------------------
+# Removendo elementos adjacentes e repetidos da lista kpath
+#----------------------------------------------------------
+i = 0
+while i < (len(kpath) -1):
+    if kpath[i] == kpath[i +1]: del kpath[i +1]
+    else: i += 1  # Avança para o próximo par de elementos
+#---------------------------------------------------------
+kpath_set = []
+for sublista in kpath:
+    if sublista not in kpath_set:
+        kpath_set.append(sublista)
+#---------------------------------
+
+
+
+#============================================================
+# Extraindo informações sobre as redes Direta e Recíproca ===
+#============================================================
+contcar = open(dir_kpath + '/CONTCAR', "r")
+VTemp = contcar.readline().split()
+n_materials = len(VTemp[1].replace('+', ' ').split())
+t_label = VTemp[-1].replace('_', ' ').split(); label = t_label[0]
+VTemp = contcar.readline(); a = float(VTemp)
+VTemp = contcar.readline().split(); A1x = float(VTemp[0])*a; A1y = float(VTemp[1])*a; A1z = float(VTemp[2])*a
+VTemp = contcar.readline().split(); A2x = float(VTemp[0])*a; A2y = float(VTemp[1])*a; A2z = float(VTemp[2])*a
+VTemp = contcar.readline().split(); A3x = float(VTemp[0])*a; A3y = float(VTemp[1])*a; A3z = float(VTemp[2])*a
+contcar.close()
+#--------------------------------
+ss1 = A1x*((A2y*A3z) - (A2z*A3y))
+ss2 = A1y*((A2z*A3x) - (A2x*A3z))
+ss3 = A1z*((A2x*A3y) - (A2y*A3x))
+ss =  ss1 + ss2 + ss3
+#-------------------------------
+B1x = ((A2y*A3z) - (A2z*A3y))/ss
+B1y = ((A2z*A3x) - (A2x*A3z))/ss 
+B1z = ((A2x*A3y) - (A2y*A3x))/ss
+B2x = ((A3y*A1z) - (A3z*A1y))/ss                             
+B2y = ((A3z*A1x) - (A3x*A1z))/ss
+B2z = ((A3x*A1y) - (A3y*A1x))/ss
+B3x = ((A1y*A2z) - (A1z*A2y))/ss
+B3y = ((A1z*A2x) - (A1x*A2z))/ss
+B3z = ((A1x*A2y) - (A1y*A2x))/ss
+#-------------------------------
+ft = 6.2831853071795860
+B1 = [B1x*ft, B1y*ft]
+B2 = [B2x*ft, B2y*ft]
+#--------------------
+
+
+
+#============================================================
+# Plot 2D da 1º Zona de Brillouin ===========================
+#============================================================
+fig, ax = plt.subplots()
+#-----------------------
+
+#-------------------------------------------------------------
+# Construindo a BZ 2D usando Voronoi (Supercélula S) ---------
+#-------------------------------------------------------------
+nx, ny = 6, 6  # Número de pontos na grade
+points = np.dot(np.mgrid[-nx:nx+1, -ny:ny+1].reshape(2, -1).T, np.array([B1, B2]))
+vor = Voronoi(points)
+#--------------------------------
+# Plotando a zona de Brillouin 2D
+#--------------------------------
+for simplex in vor.ridge_vertices:
+    simplex = np.asarray(simplex)
+    if np.all(simplex >= 0): ax.plot(vor.vertices[simplex, 0], vor.vertices[simplex, 1], color = 'black', linewidth = 0.25, alpha = 0.5, zorder=4)
+#-------------------------------------------------------------------------------------------------------------------------------------------------
+plt.quiver(0, 0, B1[0], B1[1], angles='xy', scale_units='xy', scale=1.0, color='blue', alpha = 0.5, zorder=0)
+plt.quiver(0, 0, B2[0], B2[1], angles='xy', scale_units='xy', scale=1.0, color='blue', alpha = 0.5, zorder=0)
+plt.text(B1[0]*1.0, B1[1]*1.0, "B$_1$", fontsize=10, alpha = 1.0, color="black", zorder=1)
+plt.text(B2[0]*1.0, B2[1]*1.0, "B$_2$", fontsize=10, alpha = 1.0, color="black", zorder=1)
+#-----------------------------------------------------------------------------------------
+for i in range(len(kpath) -1):
+    coord_x_1 = (kpath[i][0]*B1[0])   + (kpath[i][1]*B2[0]);   coord_x_1 = float(coord_x_1)
+    coord_y_1 = (kpath[i][0]*B1[1])   + (kpath[i][1]*B2[1]);   coord_y_1 = float(coord_y_1)
+    coord_x_2 = (kpath[i+1][0]*B1[0]) + (kpath[i+1][1]*B2[0]); coord_x_2 = float(coord_x_2) -coord_x_1
+    coord_y_2 = (kpath[i+1][0]*B1[1]) + (kpath[i+1][1]*B2[1]); coord_y_2 = float(coord_y_2) -coord_y_1
+    plt.quiver(coord_x_1, coord_y_1, coord_x_2, coord_y_2, angles='xy', scale_units='xy', scale=1.0, color='red', alpha = 0.5, zorder=2)
+#---------------------------------------------------------------------------------------------------------------------------------------
+initial_colors = ['black', 'red', 'blue', 'green', 'yellow', 'cyan', 'magenta']
+all_colors = list(matplotlib.colors.CSS4_COLORS.keys())
+remaining_colors = [color for color in all_colors if color not in initial_colors]
+color_list = (initial_colors + remaining_colors)[:len(kpath_set)]
+#----------------------------------------------------------------
+for i in range(len(kpath_set)):
+    coord_x = (kpath_set[i][0]*B1[0]) + (kpath_set[i][1]*B2[0])
+    coord_y = (kpath_set[i][0]*B1[1]) + (kpath_set[i][1]*B2[1])
+    plt.scatter(coord_x, coord_y, c=color_list[i], marker='o', s=30, edgecolor='black', linewidth=0.5, label = str(kpath_set[i][3]), zorder=3)
+#---------------------------------------------------------------------------------------------------------------------------------------------
+plt.title('1º Brillouin Zone (' + label + ')')
+plt.xlabel('kx (' + '${\AA}^{-1}$' + ' )')
+plt.ylabel('ky (' + '${\AA}^{-1}$' + ' )')
+#-----------------------------------------
+x_range = [B1[0], -B1[0], B2[0], -B2[0]]
+y_range = [B1[1], -B1[1], B2[1], -B2[1]]
+x_min = min(x_range) - abs(min(x_range))*0.1
+x_max = max(x_range) + abs(max(x_range))*0.1
+y_min = min(y_range) - abs(min(y_range))*0.1
+y_max = max(y_range) + abs(max(y_range))*0.1
+#--------------------------------------------
+plt.xlim((x_min, x_max))
+plt.ylim((y_min, y_max))
+#----------------------------------------------------
+ax.legend(loc = "lower left", title = "", fontsize=8)
+ax.set_box_aspect(abs((y_max - y_min) / (x_max - x_min)))
+#-------------------------------------------------------------------------------------------------------------------------------
+if os.path.isdir('output/Bandas'): plt.savefig('output/Bandas/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
+if os.path.isdir('output/Bandas.SO'): plt.savefig('output/Bandas.SO/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
+#-------------------------------------------------------------------------------------------------------------------------------------

{samba_ilum-1.0.0.415 → samba_ilum-1.0.0.417}/samba_ilum/src/data-base_json.py

@@ -33,18 +33,19 @@ if os.path.isfile('output/info_bands_SO.txt'):  l_file_SO = 'info_bands_SO.txt'
 if (l_file == 'null' and l_file_SO == 'null'):  sys.exit(0)
 
 
-# =========================================================
+#==========================================================
 # Extraindo o k-path para o plot da Estrutura de Bandas ===
-# =========================================================
+#==========================================================
 kpoints_file = []
 kpath = []
 #---------
 if os.path.isdir('output/Bandas'):     dir_kpath = 'bands'
 if os.path.isdir('output/Bandas.SO'):  dir_kpath = 'bands.SO'
-#-----------------------------------------------------------
+#-----------------------------------------------------------------------------
 if os.path.isfile(dir_kpath + '/' + 'KPOINTS'): kpoints_file.append('KPOINTS')
-#-------------------
-for i in range(100):
+#--------------------------------------------------------------------------------------
+nkpoints = len([file for file in os.listdir(dir_kpath) if file.startswith("KPOINTS.")])
+for i in range(nkpoints):
     file = 'KPOINTS.' + str(i+1)
     if os.path.isfile(dir_kpath + '/' + file): kpoints_file.append(file)
 #---------------------------------
@@ -227,7 +228,7 @@ coord_ions = []
 for i in range(len(type_ions)):
     for j in range(int(type_ions_n[i])):
         VTemp = poscar.readline().split()
-        coord_ions.append([ str(type_ions[i]), float(VTemp[0]), float(VTemp[1]), float(VTemp[2]) ])
+        coord_ions.append([ float(VTemp[0]), float(VTemp[1]), float(VTemp[2]), str(type_ions[i]) ])
 poscar.close()
 
 
@@ -307,7 +308,7 @@ if os.path.isfile('output/xy-scan/info_xy-scan.dat'):
    #----------------------------------------------------
    xyscan = open('output/xy-scan/info_xy-scan.dat', "r")
    #----------------------------------------------------
-   for i in range(5): VTemp = xyscan.readline().split()
+   for i in range(6): VTemp = xyscan.readline().split()
    e_slide = float(VTemp[2])
    #-------------
    xyscan.close()
@@ -708,7 +709,11 @@ for n in range(2):
                 "supercell_matrix": supercell_matrix  if n_materials > 1 else None,
                 "deformation_matrix": deformation_matrix  if n_materials > 1 else None,
                 "strain_matrix": strain_matrix  if n_materials > 1 else None,
+                # "structural_optimization": 'DFT',      # 'none', 'DFT', 'ML', 'ML/DFT'
                 "shift_plane": shift_plane if n_materials > 1 else None,
+                "z_separation": z_separation  if n_materials > 1 else None,
+                "thickness": thickness,
+                "total_thickness": total_thickness,
                 # ---------------------------------------------------------------------
                 "lattice_type": lattice_type,
                 "point_group": point_group,
@@ -721,9 +726,6 @@ for n in range(2):
                 "vdW": vdW,
                 "non_collinear": non_collinear,
                 "spin_orbit": spin_orbit,
-                "z_separation": z_separation  if n_materials > 1 else None,
-                "thickness": thickness,
-                "total_thickness": total_thickness,
                 # "param_a": param,
                 "a1": a1,
                 "a2": a2,

{samba_ilum-1.0.0.415 → samba_ilum-1.0.0.417}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.415",
+    version = "1.0.0.417",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",