SAMBA-ilum 1.0.0.403__tar.gz → 1.0.0.404__tar.gz

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.403
+Version: 1.0.0.404
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.403
+Version: 1.0.0.404
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/SAMBA_ilum.egg-info/SOURCES.txt

@@ -20,6 +20,7 @@ samba_ilum/src/bader_update.py
 samba_ilum/src/charge_transfer.py
 samba_ilum/src/chgsum.pl
 samba_ilum/src/contcar_update.py
+samba_ilum/src/data-base_json [backup].py
 samba_ilum/src/data-base_json.py
 samba_ilum/src/data-base_union.py
 samba_ilum/src/energy_scan.py

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.403'
+version = '1.0.0.404'
 
 print(" ")
 print("=============================================================")

samba_ilum-1.0.0.404/samba_ilum/src/data-base_json.py

@@ -0,0 +1,844 @@
+# SAMBA_ilum Copyright (C) 2024 - Closed source
+
+from pymatgen.io.vasp import Poscar
+from pymatgen.core import Structure
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+#--------------------------------------------------------
+import numpy as np
+import shutil
+import json
+import uuid
+import sys
+import os
+
+
+pseudo_type = 'PAW_PBE'
+exchange_correlation_functional = 'GGA'
+vdW = 'optB86b'
+
+
+# replace_type_pseudo
+# replace_type_XC
+# replace_type_vdW
+
+
+# =========================================
+# Verificando arquivos da sereme lidos: ===
+# =========================================
+l_file = 'null';  l_file_SO = 'null'
+if os.path.isfile('output/info_scf.txt'):       l_file = 'info_scf.txt'
+if os.path.isfile('output/info_bands.txt'):     l_file = 'info_bands.txt'
+if os.path.isfile('output/info_scf_SO.txt'):    l_file_SO = 'info_scf_SO.txt'
+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):
+    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('#', '')
+              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
+
+
+# ===================================================
+# Iniciando tags com valores vazios "--" ============
+# ===================================================
+area_perc_mismatch = '--';  perc_area_change = '--';  perc_mod_vectors_change = '--';
+angle_perc_mismatch = '--';  perc_angle_change = '--';  rotation_angle = '--';
+supercell_matrix = '--';  deformation_matrix = '--';  strain_matrix = '--'
+shift_plane = '--'
+
+# ============================================================
+# Extraindo informações de configuração da Heteroestrutura ===
+# ============================================================
+if os.path.isfile('output/POSCAR.info'):
+   #---------------------------------------
+   poscar = open('output/POSCAR.info', "r")
+   VTemp = poscar.readline().split()
+   param = float(poscar.readline())
+   poscar.close()
+   #------------------------
+   if (VTemp[0] == 'SAMBA'):
+      #----------------------------------------------------------------
+      l_materials = VTemp[1].replace('+', ' ').replace('_', '').split()
+      n_materials = len(l_materials)
+      #------------------------------------------
+      r_ions_materials = []; nions_materials = []
+      nion = 0;  passo = 0
+      #-----------------------------
+      for m in range(n_materials):
+          r_ions_materials.append( str(1 + nion) + ':')
+          nion += int(VTemp[m+2])
+          r_ions_materials[m] += str(nion)
+          nions_materials.append(int(VTemp[m+2]))
+      #------------------------------------------
+      id_materials = []
+      #--------------------
+
+
+      if (n_materials > 1):
+         #----------------------------------------------------------------------
+         area_perc_mismatch = []; angle_perc_mismatch = [];  rotation_angle = []
+         perc_area_change = [];  perc_mod_vectors_change = [];  perc_angle_change = []
+         supercell_matrix = [];  deformation_matrix = [];  strain_matrix = []
+         shift_plane = []
+         #---------------------
+         passo = n_materials +1
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         area_perc_mismatch.append([float(temp1[0]), float(temp1[1])])
+         if (n_materials == 3):
+            area_perc_mismatch.append([float(temp1[2]), float(temp1[3])])
+         #---------------------------------------------------------------
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         for ii in range(len(temp1)): perc_area_change.append(float(temp1[ii]))
+         #---------------------------------------------------------------------
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         perc_mod_vectors_change.append([float(temp1[0]), float(temp1[1])])
+         perc_mod_vectors_change.append([float(temp1[2]), float(temp1[3])])
+         if (n_materials == 3):
+            perc_mod_vectors_change.append([float(temp1[4]), float(temp1[5])])
+         #--------------------------------------------------------------------
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         angle_perc_mismatch.append([float(temp1[0]), float(temp1[1])])
+         if (n_materials == 3):
+            angle_perc_mismatch.append([float(temp1[2]), float(temp1[3])])
+         #----------------------------------------------------------------
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         for ii in range(len(temp1)): perc_angle_change.append(float(temp1[ii]))
+         #----------------------------------------------------------------------
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         for ii in range(len(temp1)): rotation_angle.append(float(temp1[ii]))
+         #-------------------------------------------------------------------
+         for i in range(n_materials):
+             passo += 4
+             temp1 = str(VTemp[passo]).replace('_', ' ').split()
+             supercell_matrix.append([[int(temp1[0]), int(temp1[1])], [int(temp1[2]), int(temp1[3])]])
+         #--------------------------------------------------------------------------------------------
+         for i in range(n_materials):
+             passo += 4
+             temp1 = str(VTemp[passo]).replace('_', ' ').split()
+             deformation_matrix.append([[float(temp1[0]), float(temp1[1])], [float(temp1[2]), float(temp1[3])]])
+         #------------------------------------------------------------------------------------------------------
+         for i in range(n_materials):
+             passo += 4
+             temp1 = str(VTemp[passo]).replace('_', ' ').split()
+             strain_matrix.append([[float(temp1[0]), float(temp1[1])], [float(temp1[2]), float(temp1[3])]])
+         #-------------------------------------------------------------------------------------------------
+         passo += 4
+         temp1 = str(VTemp[passo]).replace('_', ' ').split()
+         for ii in range(len(temp1)): shift_plane.append(float(temp1[ii]))
+         #----------------------------------------------------------------
+         passo += 1
+         for i in range(n_materials):
+             id_materials.append(str(VTemp[-n_materials -1 +i]))
+      #--------------------------------------------
+      temp_id = VTemp[-1].replace('_', ' ').split()
+      if (len(temp_id) > 1): estequiometria = temp_id[0]
+      id_code = VTemp[-1]
+   #-------------------------------------------------------
+   if (n_materials == 1): id_materials.append(str(id_code))
+   #-------------------------------------------------------
+   if (VTemp[0] != 'SAMBA'): exit()
+   #-------------------------------
+
+
+# ============================================================
+# Extraindo informações de configuração da Heteroestrutura ===
+# ============================================================
+poscar = open('output/POSCAR.info', "r")
+VTemp = poscar.readline().split()
+materials = VTemp[1].replace('+', ' ').split()
+#---------------------------------------------
+t_ions_materials = []
+for i in range(len(materials)):
+    ions_vector = []
+    mat_temp = materials[i].replace('_', ' ').split()
+    for j in range(len(mat_temp)): 
+        ions_vector.append(str(mat_temp[j]))
+    t_ions_materials.append(ions_vector)
+#-------------------------------------------
+for i in range(6): VTemp = poscar.readline().split()
+t_nions_materials = [];  number = -1
+for i in range(len(materials)):
+    nions_vector = []
+    mat_temp = materials[i].replace('_', ' ').split()
+    for j in range(len(mat_temp)):
+        number += 1
+        nions_vector.append(int(VTemp[number]))
+    t_nions_materials.append(nions_vector)
+#-------------
+poscar.close()
+#-------------
+
+
+# ==========================================
+# Extraindo as posições dos ions da Rede ===
+# ==========================================
+poscar = open('output/CONTCAR', "r")
+for i in range(5): VTemp = poscar.readline()
+type_ions = poscar.readline().split()
+type_ions_n = poscar.readline().split()
+poscar.readline()
+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]) ])
+poscar.close()
+
+
+# ========================================================
+# Extraindo as espessuras e separação do(s) materiais ====
+# ========================================================
+thickness = []; temp_z = [];  z_separation = []
+#----------------------------------------------
+poscar = open('output/POSCAR.info', "r")
+for i in range(8): VTemp = poscar.readline()
+for i in range(nion):
+    VTemp = poscar.readline().split()
+    temp_z.append(float(VTemp[2]))
+total_thickness = (max(temp_z) -min(temp_z))*param
+poscar.close()
+#---------------------------------------------------------
+if (n_materials == 1): thickness.append( total_thickness )
+#---------------------------------------------------------
+if (n_materials > 1):
+   poscar = open('output/POSCAR.info', "r")
+   for i in range(8): VTemp = poscar.readline()
+   for i in range(n_materials):
+       temp_z = []
+       for j in range(int(nions_materials[i])):
+           VTemp = poscar.readline().split()
+           temp_z.append(float(VTemp[2]))
+       thickness.append( (max(temp_z) -min(temp_z))*param )
+       #---------------------------------------------------------------
+       if (i > 0): z_separation.append( (min(temp_z) -temp_max)*param )
+       temp_max = max(temp_z)
+       #---------------------
+   poscar.close()   
+#----------------
+
+
+# =================================================
+# Extraindo a Energia de Ligação ==================
+# =================================================
+
+if os.path.isfile('output/z-scan/info_z-scan.dat'):
+   e_binding = '--'
+   #--------------------------------------------------
+   zscan = open('output/z-scan/info_z-scan.dat', "r")
+   #--------------------------------------------------
+   for i in range(5): VTemp = zscan.readline().split()
+   e_binding = float(VTemp[2])
+   #-------------
+   zscan.close()
+
+   # -------------------------------------
+   # Atualizando a Energia de Ligação ----
+   # -------------------------------------
+   file_oszicar   = 'relax/OSZICAR'
+   file_oszicar_f = 'relax/OSZICAR_frozen'
+   #--------------------------------------
+   if os.path.isfile(file_oszicar):
+      if os.path.isfile(file_oszicar_f):
+         #------------------------------------
+         with open(file_oszicar, 'r') as file:
+            lines = file.readlines()
+            last_line = lines[-1].split()
+            energ_r = float(last_line[2])
+         #--------------------------------------
+         with open(file_oszicar_f, 'r') as file:
+            lines = file.readlines()
+            last_line = lines[-1].split()
+            energ_f = float(last_line[2])
+         #-------------------------------
+         e_binding += (energ_f - energ_r)
+
+
+# =================================================
+# Extraindo a Energia de Deslizamento =============
+# =================================================
+if os.path.isfile('output/xy-scan/info_xy-scan.dat'):
+   e_slide = '--'
+   #----------------------------------------------------
+   xyscan = open('output/xy-scan/info_xy-scan.dat', "r")
+   #----------------------------------------------------
+   for i in range(5): VTemp = xyscan.readline().split()
+   e_slide = float(VTemp[2])
+   #-------------
+   xyscan.close()
+
+
+# ==========================================
+# Splitando o arquivo POSCAR ===============
+# ==========================================
+
+if (n_materials > 1):
+
+   #---------------------------------------
+   poscar = open('output/POSCAR.info', 'r')
+   #---------------------------------------
+   VTemp = poscar.readline().split()
+   label_materials = VTemp[1].replace('+', ' ').split()
+   n_Lattice = len(label_materials);  nion = 0
+   range_ion_Lattice = []; ntype_ions = ['']*n_Lattice           
+   #--------------------------------------------------
+   for m in range(n_Lattice):
+       range_ion_Lattice.append( str(1 + nion) + ' ')
+       nion += int(VTemp[m+2])
+       range_ion_Lattice[m] += str(nion)
+   #----------------------------------------------------
+   for m in range(6):  VTemp = poscar.readline().split()
+   #----------------------------------------------------
+   poscar.close()
+   #-------------
+   for m in range(n_Lattice):
+       contador = 0
+       for n in range(len(VTemp)):
+           contador += int(VTemp[n])
+           range_ion = range_ion_Lattice[m].split()
+           ion_i = int(range_ion[0]);  ion_f = int(range_ion[1])
+           if (contador >= ion_i and contador <= ion_f):
+              ntype_ions[m] += str(VTemp[n]) + ' '
+
+   for m in range(n_Lattice):
+       #---------------------------------------
+       poscar = open('output/POSCAR.info', 'r')
+       poscar_new = open('output/POSCAR.material_' + str(m+1), 'w')
+       #-----------------------------------------------------------
+       VTemp = poscar.readline()
+       poscar_new.write(f'POSCAR \n')
+       #-----------------------------
+       for n in range(4):
+           VTemp = poscar.readline()
+           poscar_new.write(f'{VTemp}')
+       #-------------------------------
+       VTemp = poscar.readline()
+       temp = label_materials[m].replace('_', ' ')
+       poscar_new.write(f'{temp} \n')
+       #-----------------------------
+       VTemp = poscar.readline()
+       poscar_new.write(f'{ntype_ions[m]} \n')
+       #--------------------------------------
+       VTemp = poscar.readline()
+       poscar_new.write(f'direct \n')
+       #---------------------------------------
+       range_ion = range_ion_Lattice[m].split()
+       ion_i = int(range_ion[0]);  ion_f = int(range_ion[1])
+       #----------------------------------------------------
+       for n in range(1,(nion+1)):
+           VTemp = poscar.readline()
+           if (n >= ion_i and n <= ion_f):  poscar_new.write(f'{VTemp}')
+       #----------------------------------------------------------------
+       poscar.close()
+       poscar_new.close()
+       #-----------------
+
+
+# ===============================================
+# Construindo o arquivo .json ===================
+# ===============================================
+
+#------------------------------------------------------
+# Inicializando o arquivo JSON com um dicionário vazio:
+#------------------------------------------------------
+with open('output/info.json', 'w') as file_json:
+    json.dump({}, file_json)
+
+# ===============================================
+# Atualizando as informações do arquivo .json ===
+# ===============================================
+
+for n in range(2):
+
+
+    #-------
+    crit = 1
+    #-----------
+    if (n == 0):
+       file = l_file
+       if (file == 'null'):  crit = 0
+    #-----------
+    if (n == 1):
+       file = l_file_SO
+       if (file == 'null'):  crit = 0
+    #---------
+
+
+    if (crit == 1):
+       # ===================================================
+       # Iniciando tags com valores vazios "--" ============
+       # ===================================================
+       loop = 0
+       id = '--';  id_monolayers = '--'
+       label = '--';  label_materials = '--';  formula = '--'
+       nlayers = '--';  nions = '--';  nions_monolayers = '--';  range_ions_materials = '--'
+       type_ions_materials = '--';  type_nions_materials = '--' 
+       lattice_type = '--';  point_group = [];  point_group_schoenflies = [];  space_group = [];  space_group_number = [];  inversion_symmetry = []
+       param_a = '--';  a1 = '--';  a2 = '--';  a3 = '--';  param_b = '--';  b1 = '--';  b2 = '--';  b3 = '--'
+       module_a1_a2_a3 = '--'; module_b1_b2_b3 = '--';  angle_a1a2_a1a3_a2a3 = '--'; angle_b1b2_b1b3_b2b3 = '--'
+       cell_area = '--';  cell_vol = '--';  zb_area = '--';  zb_volume = '--'
+       direct_coord_ions = '--';  k_path = '--'
+
+
+       #----------------------------------------------------------------------------------------------------------------------------------------------
+       e_vbm = '--';  e_cbm = '--';  e_fermi = '--';  e_vacuum = '--';  work_function = '--';  total_energy = '--';  e_per_ion = '--'
+       tk_vbm = '--';  tk_cbm = '--'; k_vbm = '--';  k_cbm = '--' 
+       nk = '--';  nb = '--';  ne = '--';  ne_valence = '--';  vbm = '--';  cbm = '--';  charge_transfer = [];  
+       gap = '--';  type_gap = '--';  k_vbm = [];  k_cbm = [];  lorbit = '--';  ispin = '--'
+       #------------------------------------------------------------------------------------------
+       non_collinear = '--';  spin_orbit = '--';  lorbit = '--';  ispin = '--'
+       #----------------------------------------------------------------------
+
+
+       # =========================================  ????????????????????????????????????????????????????????????????????????????????????????????????????????????
+       # Extraindo o nível de vácuo: =============  ??????????????????????????? Somente faz sentido para sistemas 2D confinados em Z ???????????????????????????
+       # =========================================  ????????????????????????????????????????????????????????????????????????????????????????????????????????????
+       l_pot = 'null';  l_pot_SO = 'null'
+       #-----------------------------------------------------------
+       if os.path.isfile('output/Potencial_bands/Potencial_Z.dat'):     l_pot = 'output/Potencial_bands/Potencial_Z.dat'
+       if os.path.isfile('output/Potencial_scf/Potencial_Z.dat'):       l_pot = 'output/Potencial_scf/Potencial_Z.dat'
+       if os.path.isfile('output/Potencial_bands_SO/Potencial_Z.dat'):  l_pot_SO = 'output/Potencial_bands_SO/Potencial_Z.dat'
+       if os.path.isfile('output/Potencial_scf_SO/Potencial_Z.dat'):    l_pot_SO = 'output/Potencial_scf_SO/Potencial_Z.dat'
+       #------------------------------------------------------------
+       if (l_pot != 'null'):
+          file0 = np.loadtxt(l_pot)
+          file0.shape
+          #-----------------
+          date_e = file0[:,1]
+          e_vacuum = max(date_e)
+       #------------------------
+       if (l_pot_SO != 'null'):
+          file1 = np.loadtxt(l_pot_SO)
+          file1.shape
+          #-----------------
+          date_e = file1[:,1]
+          e_vacuum = max(date_e) 
+
+
+       # ===========================================
+       # Extraindo dados da saída do VASProcar =====
+       # ===========================================
+       with open('output/' + file, "r") as info: lines = info.readlines()
+       #-----------------------------------------------------------------
+       for i in range(len(lines)):
+           VTemp = lines[i].replace('(', ' ( ').replace(')', ' ) ').replace(';', '').replace(',', '').split()
+           if (len(VTemp) > 0):
+              #----------------------------------------
+              if (VTemp[0] == 'LNONCOLLINEAR'):  non_collinear = str(VTemp[2])
+              #----------------------------------------
+              elif (VTemp[0] == 'LSORBIT'):  spin_orbit = str(VTemp[2])
+              #----------------------------------------
+              elif (VTemp[0] == 'nº' or VTemp[0] == 'nº'):
+                 if (VTemp[1] == 'k-points'):  nk = int(VTemp[3])
+                 if (VTemp[5] == 'bands'):  nb = int(VTemp[7])
+                 if (VTemp[1] == 'ions'):  ni = int(VTemp[3])
+                 if (VTemp[5] == 'electrons'):  ne = float(VTemp[7])
+              #----------------------------------------
+              elif (VTemp[0] == 'LORBIT'):
+                 lorbit = int(VTemp[2])
+                 if (VTemp[3] == 'ISPIN'):  ispin = int(VTemp[5])
+              #----------------------------------------
+              elif (VTemp[0] == 'Last'):  vbm = int(VTemp[4])
+              #----------------------------------------
+              elif (VTemp[0] == 'First'):  cbm = vbm +1
+              #----------------------------------------
+              elif (VTemp[0] == 'Valence'):
+                   e_vbm = float(VTemp[7])
+                   tk_vbm = int(VTemp[11])
+              #----------------------------------------
+              elif (VTemp[0] == 'Conduction'):
+                   e_cbm = float(VTemp[7])
+                   tk_cbm = int(VTemp[11])
+              #----------------------------------------
+              elif (VTemp[0] == 'GAP'):
+                type_gap = str(VTemp[2])
+                gap = float(VTemp[5])
+              #----------------------------------------
+              elif (VTemp[0] == 'Fermi'): e_fermi = float(VTemp[3])
+              #----------------------------------------
+              elif (VTemp[0] == 'free'):
+                   total_energy = float(VTemp[4])
+                   e_per_ion = total_energy/ni
+              #----------------------------------------
+              elif (VTemp[0] == 'Volume_cell'):  Volume_cell = float(VTemp[2])   
+              #----------------------------------------
+              elif (VTemp[0] == 'Param.'):  param = float(VTemp[2])   
+              #----------------------------------------
+              elif (VTemp[0] == 'A1'):
+                   a1 = [float(VTemp[4])*param, float(VTemp[5])*param, float(VTemp[6])*param]                  
+                   A1 = np.array([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])*param;  module_a1_a2_a3 = []; module_a1_a2_a3.append(np.linalg.norm(A1))
+              elif (VTemp[0] == 'A2'):
+                   a2 = [float(VTemp[4])*param, float(VTemp[5])*param, float(VTemp[6])*param]
+                   A2 = np.array([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])*param;  module_a1_a2_a3.append(np.linalg.norm(A2))
+              elif (VTemp[0] == 'A3'):
+                   a3 = [float(VTemp[4])*param, float(VTemp[5])*param, float(VTemp[6])*param]
+                   A3 = np.array([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])*param;  module_a1_a2_a3.append(np.linalg.norm(A3))
+                   #-------------------------------------------------------
+                   angle_a1a2_a1a3_a2a3 = []
+                   angle_a1a2_a1a3_a2a3.append(round(np.degrees(np.arccos(np.dot(A1,A2) / (np.linalg.norm(A1) * np.linalg.norm(A2)))), 3))
+                   angle_a1a2_a1a3_a2a3.append(round(np.degrees(np.arccos(np.dot(A1,A3) / (np.linalg.norm(A1) * np.linalg.norm(A3)))), 3))
+                   angle_a1a2_a1a3_a2a3.append(round(np.degrees(np.arccos(np.dot(A2,A3) / (np.linalg.norm(A2) * np.linalg.norm(A3)))), 3))
+              #----------------------------------------
+              elif (VTemp[0] == '2pi/Param.'):  fator_rec = float(VTemp[2])   
+              #----------------------------------------
+              elif (VTemp[0] == 'B1'):
+                   b1 = [float(VTemp[4])*fator_rec, float(VTemp[5])*fator_rec, float(VTemp[6])*fator_rec]
+                   B1 = np.array([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])*fator_rec;  module_b1_b2_b3 = []; module_b1_b2_b3.append(np.linalg.norm(B1))
+              elif (VTemp[0] == 'B2'):
+                   b2 = [float(VTemp[4])*fator_rec, float(VTemp[5])*fator_rec, float(VTemp[6])*fator_rec]
+                   B2 = np.array([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])*fator_rec;  module_b1_b2_b3.append(np.linalg.norm(B2))
+              elif (VTemp[0] == 'B3'):
+                   b3 = [float(VTemp[4])*fator_rec, float(VTemp[5])*fator_rec, float(VTemp[6])*fator_rec]
+                   B3 = np.array([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])*fator_rec;  module_b1_b2_b3.append(np.linalg.norm(B3))
+                   #-------------------------------------------------------
+                   angle_b1b2_b1b3_b2b3 = []
+                   angle_b1b2_b1b3_b2b3.append(round(np.degrees(np.arccos(np.dot(B1,B2) / (np.linalg.norm(B1) * np.linalg.norm(B2)))), 3))
+                   angle_b1b2_b1b3_b2b3.append(round(np.degrees(np.arccos(np.dot(B1,B3) / (np.linalg.norm(B1) * np.linalg.norm(B3)))), 3))
+                   angle_b1b2_b1b3_b2b3.append(round(np.degrees(np.arccos(np.dot(B2,B3) / (np.linalg.norm(B2) * np.linalg.norm(B3)))), 3))
+              #----------------------------------------
+              elif (VTemp[0] == 'Volume_ZB'):  vol_zb = float(VTemp[2])   
+              #----------------------------------------
+              elif (VTemp[0] == 'k-points'):  loop = i+3
+
+
+
+       if (tk_vbm != '--' and tk_cbm != '--'):
+          # ===========================================
+          # Buscando os pontos-k do GAP da banda ======
+          # ===========================================
+          if (file == 'info_bands.txt' or file == 'info_bands_SO.txt'):
+             if (n == 0): info = open('output/info_bands.txt', "r")
+             if (n == 1): info = open('output/info_bands_SO.txt', "r")
+             #-----------
+             test = 'nao'
+             #-----------
+             while (test == 'nao'):             
+               #--------------------------------
+               VTemp = info.readline().split()
+               #-----------------------------------------------------------
+               if (len(VTemp) > 0 and VTemp[0] == 'k-points'): test = 'sim'                       
+               #-----------------------------------------------------------
+             for nn in range(2): VTemp = info.readline()
+             for nn in range(1,(nk+1)):
+                 VTemp = info.readline().split()
+                 if (nn == int(tk_vbm)): k_vbm = [float(VTemp[1]), float(VTemp[2]), float(VTemp[3])]
+                 if (nn == int(tk_cbm)): k_cbm = [float(VTemp[1]), float(VTemp[2]), float(VTemp[3])]
+
+
+       # =================================================================
+       # Buscando os valores para a Transferência de Carga de Bader ======
+       # =================================================================
+       if (n_materials > 1):
+          #===========
+          if (n == 0):
+             if os.path.isfile('output/Charge_transfer/Bader_charge_transfer.dat'):
+                file_bader = 'output/Charge_transfer/Bader_charge_transfer.dat'
+                #----------------------------
+                bader = open(file_bader, "r")
+                for nn in range(4): VTemp = bader.readline()
+                for mn in range(len(t_ions_materials)):
+                    vector_bader = []
+                    VTemp = bader.readline()
+                    VTemp = bader.readline().split()
+                    vector_bader.append(float(VTemp[2]))
+                    for mm in range(len(t_ions_materials[mn])):
+                        VTemp = bader.readline().split()
+                        vector_bader.append(float(VTemp[3]))
+                    charge_transfer.append(vector_bader)
+          #===========
+          if (n == 1):
+             if os.path.isfile('output/Charge_transfer_SO/Bader_charge_transfer.dat'):
+                file_bader = 'output/Charge_transfer_SO/Bader_charge_transfer.dat'
+                #----------------------------
+                bader = open(file_bader, "r")
+                for nn in range(4): VTemp = bader.readline()
+                for mn in range(len(t_ions_materials)):
+                    vector_bader = []
+                    VTemp = bader.readline()
+                    VTemp = bader.readline().split()
+                    vector_bader.append(float(VTemp[2]))
+                    for mm in range(len(t_ions_materials[mn])):
+                        VTemp = bader.readline().split()
+                        vector_bader.append(float(VTemp[3]))
+                    charge_transfer.append(vector_bader)
+
+
+       """
+       # ===========================================================
+       # Obtando e organizando as informações dos pontos-k =========
+       # ===========================================================
+       if (file == 'info_bands.txt' or file == 'info_bands_SO.txt'):
+          #---------------------------------
+          info = open('output/' + file, "r")
+          #---------------------------------
+          if (loop != 0):
+             #-----------------------------------------------------
+             k_points_direct = []; k_points_cart = [];  k_path = []
+             #---------------------------------------------
+             for i in range(loop):  VTemp = info.readline()
+             for i in range(nk):
+                 VTemp = info.readline().split()
+                 k_points_direct.append([float(VTemp[1]), float(VTemp[2]), float(VTemp[3])])
+                 k_points_cart.append([float(VTemp[4]), float(VTemp[5]), float(VTemp[6])])
+                 k_path.append(float(VTemp[7]))
+          print(k_path)
+          #-----------
+          info.close()
+       """
+
+
+       # =========================================================
+       # Obtendo as simetrias da rede ============================
+       # =========================================================
+
+       #--------------------------------------------------------------------
+       # Dicionário de mapeamento de Hermann-Mauguin para Schoenflies ------
+       #--------------------------------------------------------------------
+       schoenflies = {"1": "C1",  "-1": "Ci",  "2": "C2",  "m": "Cs",  "2/m": "C2h",  "222": "D2",  "mm2": "C2v",  "mmm": "D2h",  "4": "C4",  "-4": "S4",  "4/m": "C4h",
+                      "422": "D4",  "4mm": "C4v",  "-42m": "D2d",  "4/mmm": "D4h",  "3": "C3",  "-3": "C3i",  "32": "D3",  "3m": "C3v",  "-3m": "D3d",  "6": "C6",  "-6": "C3h",  
+                      "6/m": "C6h",  "622": "D6",  "6mm": "C6v",  "-6m2": "D3h",  "6/mmm": "D6h",  "23": "T",  "m-3": "Th",  "432": "O",  "-43m": "Td",  "m-3m": "Oh"}
+       #--------------------------------------------------------------------
+       if (n_materials == 1): passo = 1
+       if (n_materials >  1): passo = n_materials +1
+       #--------------------------------------------
+       for i in range(passo):
+           #-----------------
+           if (i == 0): structure = Poscar.from_file('output/POSCAR.info').structure
+           if (i >  0): structure = Poscar.from_file('output/POSCAR.material_' + str(i)).structure
+           analyzer = SpacegroupAnalyzer(structure)
+           #----------------------------------------------------
+           point_group.append(analyzer.get_point_group_symbol())
+           space_group.append(analyzer.get_space_group_symbol())
+           space_group_number.append(analyzer.get_space_group_number())
+           inversion_symmetry.append(analyzer.is_laue())
+           if (i == 0): lattice_type = analyzer.get_lattice_type()
+           point_group_schoenflies.append(schoenflies.get(point_group[0], "Desconhecido"))
+           #------------------------------------------------------------------------------
+           # if (i > 0): os.remove('output/POSCAR.material_' + str(i)) # ERROR !!!!!!!!!!!
+
+
+       #=======================================
+       # Obtendo a área no plano XY da rede ===
+       #=======================================
+       V1 = np.array([A1[0], A1[1]])
+       V2 = np.array([A2[0], A2[1]])
+       #----------------------------
+       # Área da célula no plano XY
+       Area_cell = np.linalg.norm(np.cross(V1, V2))
+       #-------------------------------------------
+
+
+       #=======================================
+       # Obtendo a área no plano KxKy da ZB ===
+       #=======================================
+       V1 = np.array([B1[0], B1[1]])
+       V2 = np.array([B2[0], B2[1]])
+       #----------------------------
+       # Área da zb no plano KxKy
+       Area_ZB = np.linalg.norm(np.cross(V1, V2))
+       #-----------------------------------------
+
+
+       # ===========================================
+       # Criando o Dicionário ======================
+       # ===========================================
+
+       dados0 = {
+                "id": id_code,
+                "number_layers": n_materials,
+                "id_layers": id_materials,
+                "formula": estequiometria,
+                "type_ions_layers": t_ions_materials,
+                "number_ions_layers": nions_materials,
+                "number_type_ions_layers": t_nions_materials,
+                "range_ions_layers": r_ions_materials,
+                "number_ions": ni,
+                # ---------------------------------------------------------------------
+                "area_perc_mismatch": area_perc_mismatch  if n_materials > 1 else None,
+                "perc_area_change": perc_area_change  if n_materials > 1 else None,
+                "perc_mod_vectors_change": perc_mod_vectors_change  if n_materials > 1 else None,
+                "angle_perc_mismatch": angle_perc_mismatch  if n_materials > 1 else None,
+                "perc_angle_change": perc_angle_change  if n_materials > 1 else None,
+                "rotation_angle": rotation_angle  if n_materials > 1 else None,
+                "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,
+                "shift_plane": shift_plane if n_materials > 1 else None,
+                # ---------------------------------------------------------------------
+                "lattice_type": lattice_type,
+                "point_group": point_group,
+                # "point_group_schoenflies": point_group_schoenflies,
+                "space_group": space_group,
+                "space_group_number": space_group_number,
+                "inversion_symmetry": inversion_symmetry,
+                "pseudo_type": pseudo_type,
+                "exchange_correlation_functional": exchange_correlation_functional,
+                "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,
+                "a3": a3,
+                "module_a1_a2_a3": module_a1_a2_a3,
+                "angle_a1a2_a1a3_a2a3": angle_a1a2_a1a3_a2a3,
+                "cell_area": Area_cell,
+                # "cell_vol": Volume_cell,
+                # "param_b": fator_rec,
+                "b1": b1,
+                "b2": b2,
+                "b3": b3,
+                "module_b1_b2_b3": module_b1_b2_b3,
+                "angle_b1b2_b1b3_b2b3": angle_b1b2_b1b3_b2b3,
+                "zb_area": Area_ZB,
+                # "zb_volume": vol_zb,
+                "direct_coord_ions": coord_ions,
+                "kpath": kpath,
+                }
+
+
+       if (n == 0):
+          #---------
+          dados1 = {
+                   "lorbit": lorbit,
+                   "ispin": ispin,
+                   "nk": nk,
+                   "nb": nb,
+                   "ne": ne,
+                   "gap": gap,
+                   "e_vbm": e_vbm,
+                   "e_cbm": e_cbm,
+                   "vbm": vbm,
+                   "cbm": cbm,
+                   "type_gap": type_gap,
+                   "k_vbm": k_vbm,
+                   "k_cbm": k_cbm,
+                   "e_fermi": e_fermi,
+                   "e_vacuum": e_vacuum,
+                   # "work_function": work_function,
+                   "total_energy": total_energy,
+                   "e_per_ion": e_per_ion,
+                   "e_binding": e_binding  if n_materials > 1 else None,
+                   "e_slide": e_slide  if n_materials > 1 else None,
+                   "charge_transfer": charge_transfer  if n_materials > 1 else None,
+                   }
+
+
+       if (n == 1):
+          #---------
+          dados1 = {
+                   "lorbit_SO": lorbit,
+                   "ispin_SO": ispin,
+                   "nk_SO": nk,
+                   "nb_SO": nb,
+                   "ne_SO": ne,
+                   "gap_SO": gap,
+                   "e_vbm_SO": e_vbm,
+                   "e_cbm_SO": e_cbm,
+                   "vbm_SO": vbm,
+                   "cbm_SO": cbm,
+                   "type_gap_SO": type_gap,
+                   "k_vbm_SO": k_vbm,
+                   "k_cbm_SO": k_cbm,
+                   "e_fermi_SO": e_fermi,
+                   "e_vacuum_SO": e_vacuum,
+                   # "work_function_SO": work_function,
+                   "total_energy_SO": total_energy,
+                   "e_per_ion_SO": e_per_ion,
+                   "charge_transfer": charge_transfer  if n_materials > 1 else None,
+                   }
+
+
+       # ==================================================
+       # Inserindo as informações no arquivo .json ========
+       # ==================================================
+       with open('output/info.json', 'r') as file:  data = json.load(file)            # Carregando o conteúdo atual do arquivo info.json
+       data.update(dados0)                                                            # Atualizando o dicionário com as novas informações
+       with open('output/info.json', 'w') as file: json.dump(data, file, indent=4)    # Salvar o conteúdo atualizado no arquivo info.json
+       #----------------------
+       with open('output/info.json', 'r') as file:  data = json.load(file)            # Carregando o conteúdo atual do arquivo info.json
+       data.update(dados1)                                                            # Atualizando o dicionário com as novas informações
+       with open('output/info.json', 'w') as file: json.dump(data, file, indent=4)    # Salvar o conteúdo atualizado no arquivo info.json
+
+
+#===============================================================
+# Atualizando os arquivos POSCAR e CONTCAR =====================
+#===============================================================
+with open('output/POSCAR', 'r') as file: line = file.readlines()
+tline = line[0].split()
+#--------------------
+replace_line = tline[0] + ' ' + tline[1] + ' '
+for i in range(n_materials): replace_line += tline[2 +i] + ' '
+replace_line += tline[-1] + '\n'
+#------------------------------
+line[0] = replace_line
+with open('output/POSCAR', 'w') as file: file.writelines(line)
+#================================================================
+with open('output/CONTCAR', 'r') as file: line = file.readlines()
+line[0] = replace_line
+with open('output/CONTCAR', 'w') as file: file.writelines(line)
+#==============================================================
+
+
+"""
+# ===============================================
+# Abrindo e lendo o data-base .json =============
+# ===============================================
+with open('output/info.json', "r") as file_json: date = json.load(file_json)
+#------------------------------------------------
+print(" ")
+print("===========================")
+print("Dados do arquivo info.json:")
+print("===========================")
+print(" ")
+for chave, valor in date.items(): print(f"{chave}: {valor}")
+"""
+

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/samba_ilum/src/output.py

@@ -7,13 +7,13 @@ import shutil
 
 #------------------------
 current_dir = os.getcwd()
-folders = folders = [name for name in os.listdir(current_dir) if os.path.isdir(os.path.join(current_dir, name))]
-#---------------------------------------------------------------------------------------------------------------
+folders = [name for name in os.listdir(current_dir) if os.path.isdir(os.path.join(current_dir, name))]
+#-----------------------------------------------------------------------------------------------------
 if os.path.isdir('output'):
-   0 == 0
-else:
-   os.mkdir('output')
-#--------------------
+   folders2 = [name for name in os.listdir('output') if os.path.isdir(os.path.join('output', name))]
+   for i in range(len(folders2)): shutil.rmtree('output/' + folders2[i])
+else: os.mkdir('output')
+#-----------------------
 
 
 for i in range(len(folders)):
@@ -79,15 +79,3 @@ for i in range(len(folders)):
        if os.path.isdir(folders[i] + '/Charge_transfer'):    shutil.copytree(folders[i] + '/Charge_transfer',  'output/Charge_transfer_SO')
        # if os.path.isdir(folders[i] + '/Charge_transfer'):  shutil.rmtree(folders[i] + '/Charge_transfer')
     #--------------------------------
-
-
-
-
-
-
-
-
-
-
-
-

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/samba_ilum/src/xy-scan_analysis.py

@@ -308,12 +308,9 @@ 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 = ({new_delta_A1}*A1, {new_delta_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'XY_Displacement = ({x_min}, {y_min}) in Å \n')
+info.write(f'XY_Displacement = ({new_delta_A1}*A1, {new_delta_A2}*A2) \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-1.0.0.403 → samba_ilum-1.0.0.404}/samba_ilum/src/xyz-scan_analysis.py

@@ -100,8 +100,8 @@ file.close()
 info = open('info_xyz-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 = ({a1_min}*A1, {a2_min}*A2) \n')
-info.write(f'Displacement_Z = {z_min} Å \n')
+info.write(f'XY_Displacement = ({a1_min}*A1, {a2_min}*A2) \n')
+info.write(f'Z_Displacement = {z_min} Å \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-1.0.0.403 → samba_ilum-1.0.0.404}/samba_ilum/src/z-scan_analysis.py

@@ -112,7 +112,7 @@ plt.savefig('z-scan.png', dpi = 600, bbox_inches='tight', pad_inches=0)
 info = open('info_z-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_Z = {delta_z} in Å \n')
+info.write(f'Z_Displacement = {delta_z} in Å \n')
 info.write(f'------------------------------------------------------ \n')
 info.write(f'Eb = {Eb_meV:.12f} meV/Å^2  or  {Eb_J:.12f} J/m^2 \n')
 info.write(f'====================================================== \n')

{samba_ilum-1.0.0.403 → samba_ilum-1.0.0.404}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.403",
+    version = "1.0.0.404",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",