SAMBA-ilum 1.0.0.398__tar.gz → 1.0.0.399__tar.gz

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.398
+Version: 1.0.0.399
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA-ilum
-Version: 1.0.0.398
+Version: 1.0.0.399
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/SAMBA_ilum.egg-info/SOURCES.txt

@@ -32,8 +32,9 @@ samba_ilum/src/potcar.py
 samba_ilum/src/vdW_DF.py
 samba_ilum/src/xy-scan.py
 samba_ilum/src/xy-scan_analysis.py
+samba_ilum/src/xyz-scan - Copia.py
 samba_ilum/src/xyz-scan.py
-samba_ilum/src/xyz-scan_analysis.py
+samba_ilum/src/xyz-scan_analysis - Copia.py
 samba_ilum/src/z-scan.py
 samba_ilum/src/z-scan_analysis.py
 samba_ilum/src/INPUTS/INCAR_a-scan

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.398'
+version = '1.0.0.399'
 
 print(" ")
 print("=============================================================")

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/samba_ilum/src/INPUTS/SAMBA_WorkFlow.input

@@ -62,9 +62,9 @@ k_dens_z_scan = 6        # Cálculo do z-scan:  nº de pontos-k por Å-1
 #============================
 # Parâmetros xy-scan ========
 #============================
-k_dens_xy_scan = 6                                                                          # Cálculo do xy-scan:  nº de pontos-k por Å-1
-displacement_xy_A1 = [0.0, (1/8), (1/6), (1/4), (1/3), (1/2), (2/3), (3/4), (5/6), 1.0]     # Deslocamentos na direção do vetor A1 (2º material)
-displacement_xy_A2 = [0.0, (1/8), (1/6), (1/4), (1/3), (1/2), (2/3), (3/4), (5/6), 1.0]     # Deslocamentos na direção do vetor A2 (2º material)
+k_dens_xy_scan = 6                                                                     # Cálculo do xy-scan:  nº de pontos-k por Å-1
+r_displacement_A1 = [0.0, (1/8), (1/6), (1/4), (1/3), (1/2), (2/3), (3/4), (5/6)]     # Deslocamentos na direção do vetor A1 (2º material)
+r_displacement_A2 = [0.0, (1/8), (1/6), (1/4), (1/3), (1/2), (2/3), (3/4), (5/6)]     # Deslocamentos na direção do vetor A2 (2º material)
 
 
 #============================

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/samba_ilum/src/job.py

@@ -63,7 +63,7 @@ job.write(f'# module load vasp-6.2.0-gcc-9.3.0-epqgvat \n')
 job.write(f'# vasp_std="{vasp_std_2}" \n')
 job.write(f'# vasp_ncl="{vasp_ncl_2}" \n')
 job.write(f' \n') 
-job.write(f'ttasks=( "xyz-scan" "xy-scan" "z-scan" "a-scan" "relax" "scf" "bands" "dos" "bader" "scf.SO" "bands.SO" "dos.SO" "bader.SO" ) \n')
+job.write(f'ttasks=( "xyz-scan" "z-scan" "xy-scan" "a-scan" "relax" "scf" "bands" "dos" "bader" "scf.SO" "bands.SO" "dos.SO" "bader.SO" ) \n')
 job.write(f' \n')
 job.write(f'#------------------------ \n')
 job.write(f'if [ ! -d "$dir0/completed" ]; then \n')

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/samba_ilum/src/make_files.py

@@ -203,8 +203,8 @@ for i in range(len(files)):
               #===============================================================
               # Atualizando o arquivo xy-scan.py =============================
               #===============================================================
-              content = content.replace('replace_displacement_xy_A1', str(displacement_xy_A1))
-              content = content.replace('replace_displacement_xy_A2', str(displacement_xy_A2))
+              content = content.replace('replace_displacement_A1', str(r_displacement_A1))
+              content = content.replace('replace_displacement_A2', str(r_displacement_A2))
            if (task[j] == 'xyz-scan'):
               #===============================================================
               # Atualizando o arquivo xyz-scan.py ============================

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/samba_ilum/src/xy-scan.py

@@ -19,10 +19,10 @@ TALVEZ CRIAR UMA FUNÇÃO COM ESTE PROPOSITO SEJA PRATICO PARA O CODIGO TODO
 #==========================================================================
 
 # Deslocamentos a ser aplicado no 2º material, referente ao vetor A1 da rede
-displacement_A1 = [0.0, 0.125, 0.16666666666666666, 0.25, 0.3333333333333333, 0.5, 0.6666666666666666, 0.75, 0.8333333333333334]
+displacement_A1 = replace_displacement_A1
 
 # 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]
+displacement_A2 = replace_displacement_A2
 
 
 """

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/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    ??????????????????????? 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.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):
@@ -180,6 +180,8 @@ fig, ax = plt.subplots()
 cp = plt.contourf(x_grid, y_grid, e2_grid, levels = n_contour, cmap = 'jet', alpha = 1.0, antialiased = True)
 plt.quiver(0, 0, A1x, A1y, angles='xy', scale_units='xy', scale=1, color='black', label='A$_1$')
 plt.quiver(0, 0, A2x, A2y, angles='xy', scale_units='xy', scale=1, color='black', label='A$_2$')
+plt.text((A1x/2), (A1y/2), "A$_1$", fontsize=10, color="black")
+plt.text((A2x/2), (A2y/2), "A$_2$", fontsize=10, color="black")
 # plt.scatter(delta_X, delta_Y, c='black', marker='o', s=2)
 plt.scatter(x_min, y_min, c='black', marker='o', s=2)
 cbar = fig.colorbar(cp, orientation = 'vertical', shrink = 1.0)

SAMBA_ilum-1.0.0.399/samba_ilum/src/xyz-scan.py

@@ -0,0 +1,300 @@
+# SAMBA_ilum Copyright (C) 2024 - Closed source
+
+
+import numpy as np
+import shutil
+import os
+
+
+# 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 === 
+#==========================================================================
+
+# Vacuo mínimo aplicado a Heteroestrutura
+vacuo = replace_vacuo
+
+# Separação no eixo-z a ser aplicada entre os materiais da Heteroestrutura
+z_scan = replace_zscan
+
+# Deslocamentos a ser aplicado no 2º material, referente ao vetor A1 da rede
+displacement_A1 = replace_displacement_xyz_A1
+
+# Deslocamentos a ser aplicado no 2º material, referente ao vetor A2 da rede 
+displacement_A2 = replace_displacement_xyz_A2
+
+
+"""
+#----------------------------------------------------------------
+# Testando a compatibilidade do arquivo POSCAR ------------------
+#----------------------------------------------------------------
+poscar = open('POSCAR', "r")
+VTemp = poscar.readline().split()
+poscar.close()
+#-------------
+crit = 0
+for k in range(len(VTemp)):
+    try:
+       inteiro = int(VTemp[k])
+       if (k > 0 and k < 3): crit += 1
+    except ValueError:
+       if (k == 0):  crit += 1
+    #------------------------------
+    if (len(VTemp) < 3 or crit < 3):
+       print(f' ')
+       print(f'========================================')
+       print(f'Verifique o arquivo POSCAR utilizado!   ')
+       print(f'INCOMPATIBILIDADE com o código detectada')
+       print(f'========================================')
+       print(f' ')
+       #==========
+       sys.exit()   
+       #=========
+"""
+
+
+#==========================================================================
+# Obtendo os vetores de rede da Heteroestrutura ===========================
+#==========================================================================
+contcar = open('CONTCAR', "r")
+#-----------------------------
+VTemp = contcar.readline()
+VTemp = contcar.readline();  param = float(VTemp)
+VTemp = contcar.readline().split();  A1x = float(VTemp[0]);  A1y = float(VTemp[1]);  A1z = float(VTemp[2])
+VTemp = contcar.readline().split();  A2x = float(VTemp[0]);  A2y = float(VTemp[1]);  A2z = float(VTemp[2])
+VTemp = contcar.readline().split();  A3x = float(VTemp[0]);  A3y = float(VTemp[1]);  A3z = float(VTemp[2])
+#--------------
+contcar.close()
+#--------------
+
+
+#==========================================================================
+# Obtendo a altura no eixo-z dos diferentes materiais =====================
+#==========================================================================
+contcar = open('CONTCAR', "r")
+#--------------------------------
+VTemp = contcar.readline().split()
+n_Lattice = len(VTemp[1].replace('+', ' ').split())
+nions_Lattice = []
+for m in range(n_Lattice):  nions_Lattice.append(int(VTemp[m+2]))  
+#----------------------------------------------------------------
+VTemp = contcar.readline();  param = float(VTemp)
+#----------------------------------------------------
+for k in range(3): VTemp = contcar.readline().split()
+fator_Z = float(VTemp[2])*param
+#--------------------------------------------
+for k in range(3): VTemp = contcar.readline()
+#--------------------------------------------------------------
+minZ = [0]*n_Lattice;  dZ = [0]*(n_Lattice +1);  dZ_total = 0.0
+#--------------------------------------------------------------
+for k in range(n_Lattice):
+    vZ = []
+    for m in range(nions_Lattice[k]):
+        VTemp = contcar.readline().split()
+        vZ.append(float(VTemp[2]))
+    #-----------------------------
+    dZ[k+1] = (max(vZ) - min(vZ))
+    dZ_total += dZ[k+1]*fator_Z
+    minZ[k] = min(vZ)
+#--------------------
+contcar.close()
+#--------------
+
+
+#==========================================================================
+# Deslocando os materiais para Z = 0.0 ====================================
+#==========================================================================
+contcar = open('CONTCAR', "r")
+poscar_new = open('POSCAR_temp', "w")
+#------------------------------------
+for k in range(8):
+    VTemp = contcar.readline()
+    poscar_new.write(f'{VTemp}')
+for k in range(n_Lattice):
+    for m in range(nions_Lattice[k]):
+        VTemp = contcar.readline().split()
+        temp_z = float(VTemp[2]) -minZ[k] +dZ[k]
+        if (temp_z < 0.0):  temp_z = 0.0
+        poscar_new.write(f'{float(VTemp[0])} {float(VTemp[1])} {temp_z} \n')
+#-------------
+contcar.close()
+poscar_new.close()
+#-----------------
+
+
+#===========================================================
+# Convertendo as coordenadas para a forma cartesiana =======
+#===========================================================
+poscar = open('POSCAR_temp', "r")
+poscar_new = open('POSCAR_cart', "w")
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}');  VTemp = VTemp.split();  A = [float(VTemp[0]), float(VTemp[1]), float(VTemp[2])]  
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}');  VTemp = VTemp.split();  B = [float(VTemp[0]), float(VTemp[1]), float(VTemp[2])]
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}');  VTemp = VTemp.split();  C = [float(VTemp[0]), float(VTemp[1]), float(VTemp[2])]
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+VTemp = poscar.readline();  poscar_new.write(f'Cartesian \n')
+#-----------------------------------------------------------
+# Escrita das coordenadas cartesianas ----------------------
+#-----------------------------------------------------------
+for k in range(n_Lattice):
+    for m in range(nions_Lattice[k]):
+        VTemp = poscar.readline().split()
+        k1 = float(VTemp[0]); k2 = float(VTemp[1]); k3 = float(VTemp[2])
+        coord_x = ((k1*A[0]) + (k2*B[0]) + (k3*C[0]))
+        coord_y = ((k1*A[1]) + (k2*B[1]) + (k3*C[1]))
+        coord_z = ((k1*A[2]) + (k2*B[2]) + (k3*C[2]))
+        poscar_new.write(f'{coord_x:>28,.21f} {coord_y:>28,.21f} {coord_z:>28,.21f} \n')
+#-------------
+poscar.close()   
+poscar_new.close()
+#-----------------
+
+
+for z in range(len(z_scan)):
+    #-----------------
+    deltaZ = z_scan[z]
+    #-----------------
+
+    #===========================================================
+    # Gerando os arquivos POSCAR para cada separação em Z ======
+    #===========================================================
+    poscar = open('POSCAR_cart', "r")
+    poscar_new = open('POSCAR_deltaZ', "w")
+    VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+    VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+    VTemp = poscar.readline();  poscar_new.write(f'{VTemp}');  VTemp = VTemp.split();  A = [float(VTemp[0]), float(VTemp[1]), float(VTemp[2])]
+    VTemp = poscar.readline();  poscar_new.write(f'{VTemp}');  VTemp = VTemp.split();  B = [float(VTemp[0]), float(VTemp[1]), float(VTemp[2])]
+    VTemp = poscar.readline().split();  C = [float(VTemp[0]), float(VTemp[1]), float(VTemp[2])]
+    #---------------------------------------------
+    # temp_Z = (dZ_total + deltaZ_f + vacuo)/param
+    temp_Z = (dZ_total + deltaZ + vacuo)/param;  A3z = temp_Z
+    poscar_new.write(f'{float(VTemp[0]):>28,.21f} {float(VTemp[1]):>28,.21f} {float(temp_Z):>28,.21f} \n')
+    #-----------------------------------------------------------------------------------------------------
+    VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+    VTemp = poscar.readline();  poscar_new.write(f'{VTemp}')
+    VTemp = poscar.readline();  poscar_new.write(f'Cartesian \n')
+    #------------------------------------------------------------
+    for k in range(n_Lattice):
+        for m in range(nions_Lattice[k]):
+            VTemp = poscar.readline().split()
+            coord_x = float(VTemp[0]); coord_y = float(VTemp[1]); coord_z = float(VTemp[2])
+            #-------------------------------------------------------------------------------
+            coord_z = coord_z + (vacuo/2)
+            if (k > 0):  coord_z = coord_z + deltaZ
+            poscar_new.write(f'{coord_x:>28,.21f} {coord_y:>28,.21f} {coord_z:>28,.21f} \n')
+            #-------------------------------------------------------------------------------
+    #-------------
+    poscar.close()   
+    poscar_new.close()
+    #-----------------
+
+
+    #==========================================================================
+    # Gerando e Armazenando os arquivos POSCAR deslocados no plano ============
+    #==========================================================================
+    os.mkdir('POSCAR_temp_cart')
+    #---------------------------
+    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)   
+            #-----------------------------------------------
+            number += 1
+            #---------------------------------
+            poscar = open('POSCAR_deltaZ', "r")
+            poscar_new = open('POSCAR_temp_cart/POSCAR_' + str(number), "w") 
+            #---------------------------------------------------------------------------
+            VTemp = poscar.readline()
+            poscar_new.write(f'{VTemp}')
+            VTemp = VTemp.split()
+            nions1 = int(VTemp[2]);  nions2 = int(VTemp[3])
+            #----------------------------------------------
+            for k in range(7 + nions1):
+                VTemp = poscar.readline()
+                poscar_new.write(f'{VTemp}')
+            #-------------------------------
+            for k in range(nions2):
+                VTemp = poscar.readline().split()
+                poscar_new.write(f'{float(VTemp[0]) + displacement_X} {float(VTemp[1]) + displacement_Y} {VTemp[2]} \n')
+            #-----------------------------------------------------------------------------------------------------------
+            poscar.close()
+            poscar_new.close()
+            #-----------------
+
+
+    #=============================================================================
+    # Convertendo as coordenadas dos arquivos POSCAR de cartesiano para direto ===
+    #=============================================================================
+
+    #---------
+    number = 0
+    #----------
+    a = np.array([A1x*param, A1y*param, A1z*param])
+    b = np.array([A2x*param, A2y*param, A2z*param])
+    c = np.array([A3x*param, A3y*param, A3z*param])
+    T = np.linalg.inv(np.array([a, b, c]).T)  # Definindo a matriz de transformação
+    #------------------------------------------------------------------------------
+
+    for ii in displacement_A1:
+        for jj in displacement_A2: 
+            #----------
+            number += 1
+            #---------------------------------
+            dir_temp = str(ii) + '_' + str(jj) + '_' + str(deltaZ)
+            os.mkdir(dir_temp)
+            if os.path.isfile('vdw_kernel.bindat'): shutil.copyfile('vdw_kernel.bindat', dir_temp + '/vdw_kernel.bindat')
+            shutil.copyfile('contcar_update.py', dir_temp + '/contcar_update.py')
+            shutil.copyfile('energy_scan.py', dir_temp + '/energy_scan.py')
+            shutil.copyfile('KPOINTS', dir_temp + '/KPOINTS')
+            shutil.copyfile('POTCAR', dir_temp + '/POTCAR')
+            shutil.copyfile('INCAR', dir_temp + '/INCAR')
+            #-----------------------------------------------------------
+            poscar = open('POSCAR_temp_cart/POSCAR_' + str(number), "r")
+            poscar_new = open(dir_temp + '/POSCAR', "w") 
+            #-------------------------------------------
+            for k in range(7):
+                VTemp = poscar.readline()
+                poscar_new.write(f'{VTemp}')
+            #------------------------
+            VTemp = poscar.readline()
+            poscar_new.write(f'Direct \n')
+
+            #----------------------------------------------------------------------------------------------------
+            # Convertendo as posições atomicas cartesianas de todos os átomos da Supercélula para a forma direta,
+            # e ajustando as posições dos átomos que se encontram fora da célula.
+            #--------------------------------------------------------------------
+            for k in range(nions1 + nions2):
+                VTemp = poscar.readline().split()
+                x = float(VTemp[0])
+                y = float(VTemp[1])
+                z = float(VTemp[2])    
+                #----------------------
+                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):
+                       f[m] = 0.0
+                poscar_new.write(f'{f[0]} {f[1]} {f[2]} \n')
+
+
+            #-------------
+            poscar.close()
+            poscar_new.close()
+    #------------------------
+    os.remove('POSCAR_deltaZ')
+    shutil.rmtree('POSCAR_temp_cart')
+#------------------------------------
+os.remove('POSCAR_temp')
+os.remove('POSCAR_cart')
+#-----------------------

{SAMBA_ilum-1.0.0.398 → SAMBA_ilum-1.0.0.399}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.398",
+    version = "1.0.0.399",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",