SAMBA-ilum 1.0.0.523__tar.gz → 1.0.0.524__tar.gz

{samba_ilum-1.0.0.523 → samba_ilum-1.0.0.524}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.523
+Version: 1.0.0.524
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.523 → samba_ilum-1.0.0.524}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.523
+Version: 1.0.0.524
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.523 → samba_ilum-1.0.0.524}/SAMBA_ilum.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ samba_ilum/src/charge_transfer.py
 samba_ilum/src/chgsum.pl
 samba_ilum/src/contcar_update.py
 samba_ilum/src/data-base_json.py
+samba_ilum/src/data-base_json_fix.py
 samba_ilum/src/data-base_union.py
 samba_ilum/src/energy_scan.py
 samba_ilum/src/hubbard_correction.py

{samba_ilum-1.0.0.523 → samba_ilum-1.0.0.524}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.523'
+version = '1.0.0.524'
 
 print(" ")
 print("=============================================================")

{samba_ilum-1.0.0.523 → samba_ilum-1.0.0.524}/samba_ilum/src/HeteroStructure_Generator.py

@@ -1842,91 +1842,6 @@ for i in range(len(files0)):
     #--------------------------------
 
 
-#=====================================================================
-# Renaming POSCAR files for better data organization =================
-#=====================================================================
-# coord_direct = [0.0, 0.1, (2/9), (1/6), 0.2, (2/9), 0.25, 0.3, (1/3), 0.4, (4/9), 0.5, (5/9), 0.6, (2/3), 0.7, (7/9), 0.75, 0.8, (8/9), (5/6), 0.9, (9/9), 1.0]
-files = os.listdir(diret2)
-#--------------------------
-for i in range(len(files)):
-    #------------------------------------
-    poscar = open(diret2 + files[i], "r")
-    #------------------------------------ 
-    VTemp = poscar.readline().split()
-    if (n_Lattice == 2):
-       var_area = str(VTemp[11])
-       rotation_angle = str(VTemp[27])
-    if (n_Lattice == 3):
-       var_area = str(VTemp[12])
-       rotation_angle = str(VTemp[28])
-
-    #-------------------------
-    VTemp1 = VTemp[-1].split()
-    #-------------------------
-
-    #-------------------------------------------------------
-    VTemp = poscar.readline()
-    param = float(VTemp)
-    #-------------------------------------------------------
-    A = poscar.readline().split()
-    B = poscar.readline().split()
-
-    for ii in range(3): VTemp = poscar.readline().split()
-    nion = 0
-    for j in range(len(VTemp)):  nion += int(VTemp[j])
-    if (nion < 10):                  n_ion = '00' + str(nion) + 'atoms'
-    if (nion >= 10 and nion < 100):  n_ion = '0'  + str(nion) + 'atoms'
-    if (nion >= 100):                n_ion = ''   + str(nion) + 'atoms'
-    #------------------------------------------------------------------
-    poscar.close()
-    #-------------
-
-    #-------------------------------------------------------------
-    if ((i+1) < 10):                     number = '000' + str(i+1)
-    if ((i+1) >= 10  and (i+1) < 100):   number = '00'  + str(i+1)
-    if ((i+1) >= 100 and (i+1) < 1000):  number = '0'   + str(i+1)
-    if ((i+1) >= 1000):                  number = ''    + str(i+1) 
-    #-------------------------------------------------------------
-
-    #-------------------------------------
-    current_name = diret2 + files[i]
-    if (n_Lattice == 2):
-       new_name = diret2 + n_ion + '_' + var_area + '_' + rotation_angle + '_' + str(VTemp1[-1]) + '+' + number + '.vasp'
-    if (n_Lattice == 3):
-       new_name = diret2 + n_ion + '_' + var_area + '_' + rotation_angle + '_'+ str(VTemp1[-1]) + '+' + number + '.vasp'
-    os.rename(current_name, new_name)
-    #--------------------------------
-
-    #---------------------------
-    poscar = open(new_name, "r")
-    VTemp = poscar.readline().split()
-    poscar.close()
-    #-------------
-    t_VTemp = ''
-    for ii in range(len(VTemp) -1):
-        t_VTemp += str(VTemp[ii]) + ' '
-    if (n_Lattice > 1): 
-       for ii in range(n_Lattice): t_VTemp += id_materials[ii] + ' ' 
-    t_VTemp += str(VTemp[len(VTemp)-1])
-    #=-------------------------------------------------------
-    with open(new_name, 'r') as file: line = file.readlines()
-    #=-------------------------------------------------------
-    line[0] = t_VTemp + '+' + number + '\n'
-    #--------------------------------------
-    """
-    for ii in range(nion):
-        VTemp = line[8+ii].split()
-        for ij in range(3):
-            VTemp[ij] = float(VTemp[ij])
-            for ik in range(len(coord_direct)):
-                if (abs(VTemp[ij] -coord_direct[ik]) < 0.0001): VTemp[ij] = coord_direct[ik]
-        line[8+ii] = str(VTemp[0]) + ' ' + str(VTemp[1]) + ' ' + str(VTemp[2]) + '\n'
-    """
-    #------------------------------------------------------
-    with open(new_name, 'w') as file: file.writelines(line)
-    #------------------------------------------------------
-
-
 #=====================================================================
 # Filtering/Excluding Similar POSCAR Files ===========================
 #=====================================================================
@@ -2039,6 +1954,90 @@ if (n_structures >  1): print(f'{n_structures} cells were found')
 print(f'============================================')
 
 
+#=====================================================================
+# Renaming POSCAR files for better data organization =================
+#=====================================================================
+files = os.listdir(diret2)
+#--------------------------
+for i in range(len(files)):
+    #------------------------------------
+    poscar = open(diret2 + files[i], "r")
+    #------------------------------------ 
+    VTemp = poscar.readline().split()
+    if (n_Lattice == 2):
+       var_area = str(VTemp[11])
+       rotation_angle = str(VTemp[27])
+    if (n_Lattice == 3):
+       var_area = str(VTemp[12])
+       rotation_angle = str(VTemp[28])
+
+    #-------------------------
+    VTemp1 = VTemp[-1].split()
+    #-------------------------
+
+    #-------------------------------------------------------
+    VTemp = poscar.readline()
+    param = float(VTemp)
+    #-------------------------------------------------------
+    A = poscar.readline().split()
+    B = poscar.readline().split()
+
+    for ii in range(3): VTemp = poscar.readline().split()
+    nion = 0
+    for j in range(len(VTemp)):  nion += int(VTemp[j])
+    if (nion < 10):                  n_ion = '00' + str(nion) + 'atoms'
+    if (nion >= 10 and nion < 100):  n_ion = '0'  + str(nion) + 'atoms'
+    if (nion >= 100):                n_ion = ''   + str(nion) + 'atoms'
+    #------------------------------------------------------------------
+    poscar.close()
+    #-------------
+
+    #-------------------------------------------------------------
+    if ((i+1) < 10):                     number = '000' + str(i+1)
+    if ((i+1) >= 10  and (i+1) < 100):   number = '00'  + str(i+1)
+    if ((i+1) >= 100 and (i+1) < 1000):  number = '0'   + str(i+1)
+    if ((i+1) >= 1000):                  number = ''    + str(i+1) 
+    #-------------------------------------------------------------
+
+    #-------------------------------------
+    current_name = diret2 + files[i]
+    if (n_Lattice == 2):
+       new_name = diret2 + n_ion + '_' + var_area + '_' + rotation_angle + '_' + str(VTemp1[-1]) + '+' + number + '.vasp'
+    if (n_Lattice == 3):
+       new_name = diret2 + n_ion + '_' + var_area + '_' + rotation_angle + '_'+ str(VTemp1[-1]) + '+' + number + '.vasp'
+    os.rename(current_name, new_name)
+    #--------------------------------
+
+    #---------------------------
+    poscar = open(new_name, "r")
+    VTemp = poscar.readline().split()
+    poscar.close()
+    #-------------
+    t_VTemp = ''
+    for ii in range(len(VTemp) -1):
+        t_VTemp += str(VTemp[ii]) + ' '
+    if (n_Lattice > 1): 
+       for ii in range(n_Lattice): t_VTemp += id_materials[ii] + ' ' 
+    t_VTemp += str(VTemp[len(VTemp)-1])
+    #=-------------------------------------------------------
+    with open(new_name, 'r') as file: line = file.readlines()
+    #=-------------------------------------------------------
+    line[0] = t_VTemp + '_' + str(nion) + 'atoms' + '+' + number + '\n'
+    #------------------------------------------------------------------
+    """
+    for ii in range(nion):
+        VTemp = line[8+ii].split()
+        for ij in range(3):
+            VTemp[ij] = float(VTemp[ij])
+            for ik in range(len(coord_direct)):
+                if (abs(VTemp[ij] -coord_direct[ik]) < 0.0001): VTemp[ij] = coord_direct[ik]
+        line[8+ii] = str(VTemp[0]) + ' ' + str(VTemp[1]) + ' ' + str(VTemp[2]) + '\n'
+    """
+    #------------------------------------------------------
+    with open(new_name, 'w') as file: file.writelines(line)
+    #------------------------------------------------------
+
+
 #=====================================================================
 # Adjusting direct coordinates of lattices ===========================
 #=====================================================================