SAMBA-ilum 1.0.0.416__tar.gz → 1.0.0.418__tar.gz

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.416
+Version: 1.0.0.418
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.416
+Version: 1.0.0.418
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/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-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.416'
+version = '1.0.0.418'
 
 print(" ")
 print("=============================================================")

samba_ilum-1.0.0.418/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/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
+if os.path.isdir('output/Bandas_SO'): plt.savefig('output/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
+#---------------------------------------------------------------------------------------------------------------------------

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/src/INPUTS/INCAR_xy-scan

@@ -1,6 +1,6 @@
 SYSTEM = "VASP"
 NELMIN = 4
-NELM = 60
+NELM = 120
 EDIFF = 1E-6
 EDIFFG = -1E-3
 # replace_ispin

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/src/INPUTS/INCAR_xyz-scan

@@ -1,6 +1,6 @@
 SYSTEM = "VASP"
 NELMIN = 4
-NELM = 60
+NELM = 120
 EDIFF = 1E-6
 EDIFFG = -1E-3
 # replace_ispin

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/src/INPUTS/INCAR_z-scan

@@ -1,6 +1,6 @@
 SYSTEM = "VASP"
 NELMIN = 4
-NELM = 60
+NELM = 120
 EDIFF = 1E-6
 EDIFFG = -1E-3
 # replace_ispin

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/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()
 
 
@@ -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-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/src/job.py

@@ -45,6 +45,10 @@ job = open(dir_out + '/job0.sh', "w")
 #====================================
 job.write(f'#!/bin/bash \n')
 job.write(f' \n')
+job.write(f'cd $dir0 \n'
+job.write(f'mv python_virtual python_virtual_delete \n'
+job.write(f'rm -r python_virtual_delete \n'
+job.write(f' \n')
 job.write(f'#------------------------------- \n')
 job.write(f'dir_virtual="{dir_virtual_python}" \n')
 job.write(f'# cp -r $dir_virtual $dir0/python_virtual \n')

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/src/xy-scan.py

@@ -78,8 +78,8 @@ for i in range(len(folders)):  shutil.rmtree('folders[i]')
 poscar = open('POSCAR', "r")
 #---------------------------------
 line_0 = poscar.readline().split()
-if (line_0[-5] == 'Shift_plane'):  shift = str(line_0[-5])
-if (line_0[-5] != 'Shift_plane'):  shift = '0.0_0.0'
+if (line_0[-7] == 'Shift_plane'):  shift = str(line_0[-5])
+if (line_0[-7] != 'Shift_plane'):  shift = '0.0_0.0'
 #-----------------------------------------------
 VTemp = poscar.readline();  param = float(VTemp)
 VTemp = poscar.readline().split();  A1x = float(VTemp[0]);  A1y = float(VTemp[1]);  A1z = float(VTemp[2])

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/samba_ilum/src/xy-scan_analysis.py

@@ -23,6 +23,7 @@ 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.patheffects as path_effects
 import matplotlib.colors as mcolors
 #----------------------------------
 
@@ -69,14 +70,10 @@ 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
-#-------------------------------
+#--------------------------------
 
 
 #===============================================
@@ -102,7 +99,7 @@ for i in range(len(date_shift)):
             t_shift_A1 = shift_A1 -a1_min +shift[j]
             t_shift_A2 = shift_A2 -a2_min +shift[k]
             if (t_shift_A1 >= -0.2  and t_shift_A1 <= 1.2):
-               if (t_shift_A2 >= -0.2  and t_shift_A2 <= 1.2): 
+               if (t_shift_A2 >= -0.2  and t_shift_A2 <= 1.2):
                   file.write(f'{t_shift_A1}_{t_shift_A2} {(date_E[i]*1000)/Area} \n')
 #-----------
 file.close()
@@ -126,7 +123,7 @@ 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]*1000)/Area} \n')
+    file.write(f'{VTemp} {date_E[i]} \n')
 #-----------
 file.close()
 #-----------
@@ -140,7 +137,7 @@ for i in range(len(date_shift)):
     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]*1000)/Area} \n')
+    file.write(f'{Coord_X} {Coord_Y} {date_E[i]} \n')
 #-----------
 file.close()
 #-----------
@@ -225,14 +222,14 @@ cmap_gray = (mpl.colors.ListedColormap(['darkgray', 'darkgray']))
 #-----------------------
 fig, ax = plt.subplots()
 cp = plt.contourf(x_grid, y_grid, (e2_grid -E_min), 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.quiver(0, 0, A1x, A1y, angles='xy', scale_units='xy', scale=1, color='red', label='A$_1$', linewidth=0.1, edgecolor='black')
+plt.quiver(0, 0, A2x, A2y, angles='xy', scale_units='xy', scale=1, color='red', label='A$_2$', linewidth=0.1, edgecolor='black')
 plt.plot([A1x, (A1x+A2x)], [A1y, (A1y+A2y)], color = 'black', linewidth = 1.0, zorder=3)
 plt.plot([A2x, (A1x+A2x)], [A2y, (A1y+A2y)], color = 'black', linewidth = 1.0, zorder=3)
-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)
+text1 = plt.text((A1x/2), (A1y/2), "A$_1$", fontsize=10, color="red")
+text2 = plt.text((A2x/2), (A2y/2), "A$_2$", fontsize=10, color="red")
+text1.set_path_effects([path_effects.Stroke(linewidth=0.2, foreground='black'), path_effects.Normal()])
+text2.set_path_effects([path_effects.Stroke(linewidth=0.2, foreground='black'), path_effects.Normal()])
 cbar = fig.colorbar(cp, orientation = 'vertical', shrink = 1.0)
 #-------------------
 plt.title('xy-scan')
@@ -255,16 +252,31 @@ shutil.copyfile(str(delta) + '/CONTCAR', 'CONTCAR')
 #--------------------------------------------------
 
 
+#-----------------------------
+contcar = open('CONTCAR', "r")
+#----------------------------------
+line_0 = contcar.readline().split()
+if (line_0[-7] == 'Shift_plane'):
+   shift_0 = str(line_0[-5])
+   shift_0 = shift_0.replace('_', ' ').split()
+   #------------------------------------------
+   shift_A1 = float(shift_0[0])
+   shift_A2 = float(shift_0[1])
+   shift_X = (shift_A1*A1x) + (shift_A2*A2x)
+   shift_Y = (shift_A1*A1y) + (shift_A2*A2y)
+   #----------------------------------------
+contcar.close()
+#--------------
+
+
 #=====================================================
 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 = ({shift_X}, {shift_Y}) in Å \n')
+info.write(f'Displacement_XY = ({shift_A1}*A1, {shift_A2}*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')

{samba_ilum-1.0.0.416 → samba_ilum-1.0.0.418}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.416",
+    version = "1.0.0.418",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",