SAMBA-ilum 1.0.0.394__tar.gz → 1.0.0.395__tar.gz

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.394
+Version: 1.0.0.395
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA-ilum
-Version: 1.0.0.394
+Version: 1.0.0.395
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.394'
+version = '1.0.0.395'
 
 print(" ")
 print("=============================================================")

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/INPUTS/SAMBA_HeteroStructure.input

@@ -48,6 +48,8 @@ crit_area = 5                          # Variação perc. % da área das redes q
 #----------------------------------
 ions_crit_i = 1                        # Critério para o nº mínimo de átomos permitido na Heteroestrutura.
 ions_crit_f = 100                      # Critério para o nº máximo de átomos permitido na Heteroestrutura.
+                                       # Observação: Ao fazer o loop de muitas estruturas, aconselho varrer pequenos ranges de ions
+                                       #             por exemplo:  (1, 10);  (10, 20);  (50,60) 
 #----------------------------------
                                        # Por padrão sempre teremos: angle > 0.0 and angle < 180.0
 angle_min = 15.0                       # Angulo minímo de abertura entre os vetores A1 e A2

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/INPUTS/SAMBA_WorkFlow.input

@@ -14,7 +14,7 @@ replace_type_pseudo = 'PAW_PBE'; replace_type_XC = 'GGA'
 
 
 #=======================================================
-tasks = ['relax', 'scf', 'bands', 'dos']    # tasks = ['xyz-scan', 'xy-scan', 'z-scan', 'a-scan', 'relax', 'scf', 'bands', 'dos', 'bader']
+tasks = ['relax', 'scf', 'bands', 'dos']    # tasks = ['z-scan', 'xy-scan', 'relax', 'scf', 'bands', 'dos', 'bader']
 type  = ['sem_SO','com_SO']                 # type  = ['sem_SO','com_SO']
 #=======================================================
 dipol = 'none'            # Utilize as opções:  'none',  'center_cell'  or  'center_mass'

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.bands

@@ -50,7 +50,7 @@ esc_fermi = 1
 # [0] NOT                                                       
 # [1] YES                                                       
 ################################################################
-esc_range_E = 0
+esc_range_E = 1
 
 if (esc_range_E == 1):
    ################################################################ 
@@ -62,7 +62,7 @@ if (esc_range_E == 1):
    # '-3.0 15.0'                                       
    # '-5.1 5.0'                                         
    ################################################################      
-   range_E = '-1.0 1.0'
+   range_E = '-5.0 5.0'
 
 
 

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.location

@@ -106,7 +106,7 @@ esc_fermi = 1
 # [0] NOT                                                       
 # [1] YES                                                       
 ################################################################
-esc_range_E = 0
+esc_range_E = 1
 
 if (esc_range_E == 1):
    ################################################################ 
@@ -118,7 +118,7 @@ if (esc_range_E == 1):
    # '-3.0 15.0'                                        
    # '-5.1 5.0'                                         
    ################################################################      
-   range_E = '-1.0 1.0' 
+   range_E = '-5.0 5.0' 
 
 
 

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.orbitals

@@ -51,7 +51,7 @@ esc_fermi = 1
 # [0] NOT                                                       
 # [1] YES                                                       
 ################################################################
-esc_range_E = 0
+esc_range_E = 1
 
 if (esc_range_E == 1):
    ################################################################ 
@@ -63,7 +63,7 @@ if (esc_range_E == 1):
    # '-3.0 15.0'                                        
    # '-5.1 5.0'                                         
    ################################################################      
-   range_E = '-1.0 1.0' 
+   range_E = '-5.0 5.0' 
 
 
 

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.spin

@@ -80,7 +80,7 @@ fyx2=1; fxyz=1; fyz2=1; fzz2=1; fxz2=1; fzx2=1; fxx2=1
 # [0] NOT                                                       
 # [1] YES                                                       
 ################################################################
-esc_range_E = 0
+esc_range_E = 1
 
 if (esc_range_E == 1):
    ################################################################ 
@@ -92,7 +92,7 @@ if (esc_range_E == 1):
    # -3.0 15.0                                        
    # -5.1 5.0                                         
    ################################################################      
-   range_E = '-1.0 1.0'  
+   range_E = '-5.0 5.0'  
   
 
 

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/energy_scan.py

@@ -19,4 +19,12 @@ energia = VTemp.replace('=',' ').split()
 
 energy.write(f'{name_dir} {energia[4]} \n')
 
+temp_name = name_dir.replace('_', ' ').split()
+if (len(temp_name) == 2):
+   if (temp_name[0] == '0.0'): temp_name[0] = '1.0'
+   if (temp_name[1] == '0.0'): temp_name[1] = '1.0'
+   if (temp_name[0] == '1.0' or temp_name[1] == '1.0'):
+      new_name_dir == str(temp_name[0]) + '_' + str(temp_name[1])
+      energy.write(f'{new_name_dir} {energia[4]} \n')
+
 energy.close()

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/xy-scan.py

@@ -9,20 +9,20 @@ import os
 """
 INSERIR FUNÇÃO PARA VERIFICAR SE O ARQUIVO POSCAR INICIAL ESTA ESCRITO EM COORDENADAS DIRETAS OU CARTESIANAS
 SE ESTIVER ESCRITO EM COORDENADAS DIRETAS, CONVERTER PARA COORDENADAS CARTESIANAS
-TALVEZ CRIAR UMA FUNÇÃO COM ESTE PROPOSITO SEJA PRATICO PARA O CODIGO TODO 
+TALVEZ CRIAR UMA FUNÇÃO COM ESTE PROPOSITO SEJA PRATICO PARA O CODIGO TODO
 """
 
 
 # Atenção: ================================================================
 # O código foi escrito pensado em uma Heteroestrutura com n_Lattice = 2 ===
-# Para redes com n_Lattice > 2 testes e generalizações devem ser feitas === 
+# Para redes com n_Lattice > 2 testes e generalizações devem ser feitas ===
 #==========================================================================
 
 # Deslocamentos a ser aplicado no 2º material, referente ao vetor A1 da rede
-displacement_A1 = replace_displacement_xy_A1
+displacement_A1 = [0.0, 0.125, 0.16666666666666666, 0.25, 0.3333333333333333, 0.5, 0.6666666666666666, 0.75, 0.8333333333333334]
 
-# Deslocamentos a ser aplicado no 2º material, referente ao vetor A2 da rede    
-displacement_A2 = replace_displacement_xy_A2
+# Deslocamentos a ser aplicado no 2º material, referente ao vetor A2 da rede
+displacement_A2 = [0.0, 0.125, 0.16666666666666666, 0.25, 0.3333333333333333, 0.5, 0.6666666666666666, 0.75, 0.8333333333333334]
 
 
 """
@@ -49,7 +49,7 @@ for k in range(len(VTemp)):
        print(f'========================================')
        print(f' ')
        #==========
-       sys.exit()   
+       sys.exit()
        #=========
 """
 
@@ -76,8 +76,11 @@ for i in range(len(folders)):  shutil.rmtree('folders[i]')
 # Obtendo os vetores de rede da Heteroestrutura ===========================
 #==========================================================================
 poscar = open('POSCAR', "r")
-#---------------------------
-VTemp = poscar.readline()
+#---------------------------------
+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'
+#-----------------------------------------------
 VTemp = poscar.readline();  param = float(VTemp)
 VTemp = poscar.readline().split();  A1x = float(VTemp[0]);  A1y = float(VTemp[1]);  A1z = float(VTemp[2])
 VTemp = poscar.readline().split();  A2x = float(VTemp[0]);  A2y = float(VTemp[1]);  A2z = float(VTemp[2])
@@ -97,17 +100,30 @@ number = 0
 for ii in displacement_A1:
     for jj in displacement_A2:
         #-----------------------------------------------
-        displacement_X = (ii*A1x*param) + (jj*A2x*param)        
-        displacement_Y = (ii*A1y*param) + (jj*A2y*param)   
+        displacement_X = (ii*A1x*param) + (jj*A2x*param)
+        displacement_Y = (ii*A1y*param) + (jj*A2y*param)
         #-----------------------------------------------
         number += 1
         #---------------------------
         poscar = open('POSCAR', "r")
-        poscar_new = open('POSCAR_temp_cart/POSCAR_' + str(number), "w") 
+        poscar_new = open('POSCAR_temp_cart/POSCAR_' + str(number), "w")
         #---------------------------------------------------------------------------
-        VTemp = poscar.readline()
-        poscar_new.write(f'{VTemp}')
-        VTemp = VTemp.split()
+        VTemp = poscar.readline().split()
+        #-----------
+        temp_shift = shift.replace('_', ' ').split()
+        shift_A1 = float(temp_shift[0]) + float(ii)
+        shift_A2 = float(temp_shift[1]) + float(jj)
+        for k in range(3):
+            if (shift_A1 > 1.0): shift_A1 = shift_A1 -1.0
+            if (shift_A2 > 1.0): shift_A2 = shift_A2 -1.0
+        if (shift_A1 == 1.0): shift_A1 = 0.0
+        if (shift_A2 == 1.0): shift_A2 = 0.0
+        new_shift = str(shift_A1) + '_' + str(shift_A2)
+        line_0[-5] = new_shift
+        #-----------
+        for k in range(len(line_0)):  poscar_new.write(f'{line_0[k]} ')
+        poscar_new.write(f' \n')
+        #----------------------------------------------
         nions1 = int(VTemp[2]);  nions2 = int(VTemp[3])
         #----------------------------------------------
         for k in range(7 + nions1):
@@ -137,7 +153,7 @@ T = np.linalg.inv(np.array([a, b, c]).T)  # Definindo a matriz de transformaçã
 #------------------------------------------------------------------------------
 
 for ii in displacement_A1:
-    for jj in displacement_A2: 
+    for jj in displacement_A2:
         #----------
         number += 1
         #---------------------------------
@@ -151,7 +167,7 @@ for ii in displacement_A1:
         shutil.copyfile('INCAR', dir_temp + '/INCAR')
         #-----------------------------------------------------------
         poscar = open('POSCAR_temp_cart/POSCAR_' + str(number), "r")
-        poscar_new = open(dir_temp + '/POSCAR', "w") 
+        poscar_new = open(dir_temp + '/POSCAR', "w")
         #-------------------------------------------
         for k in range(7):
             VTemp = poscar.readline()
@@ -168,15 +184,15 @@ for ii in displacement_A1:
             VTemp = poscar.readline().split()
             x = float(VTemp[0])
             y = float(VTemp[1])
-            z = float(VTemp[2])    
+            z = float(VTemp[2])
+            #----------------------
+            r = np.array([x, y, z])        # Definindo o vetor posição cartesiano do átomo
             #----------------------
-            r = np.array([x, y, z])        # Definindo o vetor posição cartesiano do átomo  
-            #----------------------           
             f = np.dot(T, r)               # Calculando a correspondenre posição em coordenadas fracionárias
             for m in range(3):
                 f = np.where(f < 0, f + 1, f)
                 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):
@@ -195,3 +211,4 @@ for ii in displacement_A1:
 # os.remove('INCAR')
 
 shutil.rmtree('POSCAR_temp_cart')
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/samba_ilum/src/xy-scan_analysis.py

@@ -152,9 +152,9 @@ T = np.linalg.inv(np.array([a, b, c]).T)  # Definindo a matriz de transformaçã
 #------------------------------------------------------------------------------
 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
-for m in range(3):
-    f = np.where(f < 0, f + 1, f)
+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):

{SAMBA_ilum-1.0.0.394 → SAMBA_ilum-1.0.0.395}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.394",
+    version = "1.0.0.395",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",