SAMBA-ilum 1.0.0.540__tar.gz → 1.0.0.542__tar.gz

{samba_ilum-1.0.0.540 → samba_ilum-1.0.0.542}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.540
+Version: 1.0.0.542
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.540 → samba_ilum-1.0.0.542}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.540
+Version: 1.0.0.542
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.540 → samba_ilum-1.0.0.542}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.540'
+version = '1.0.0.542'
 
 print(" ")
 print("=============================================================")

{samba_ilum-1.0.0.540 → samba_ilum-1.0.0.542}/samba_ilum/src/HeteroStructure_Generator.py

@@ -37,10 +37,10 @@ if (crit_area <= 0.0):             crit_area = 0.01
 #-----------------------------------------------------------------------------------------------------------------------------------------------
 letters     = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'X', 'Z', 'Y', 'W']
 alphabet    = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'X', 'Z', 'Y', 'W']
-#--------------------------------------------------
-# Generating 1066 temporary labels for lattice ions
-#--------------------------------------------------
-for k in range(40):
+#---------------------------------------------------
+# Generating 26026 temporary labels for lattice ions
+#---------------------------------------------------
+for k in range(1000):
     for i in range(len(letters)):
         alphabet.append(letters[i] + str(k+1))      
 #--------------------------------------------------------------------------------------------------------------------
@@ -1707,6 +1707,7 @@ print(f'{n_structures} remaining cells')
 
 #=====================================================================
 # Filtering/Excluding Similar POSCAR Files ===========================
+# within the temporary subdirectories of the POSCAR files ============
 #=====================================================================
 
 n += 1
@@ -1825,7 +1826,7 @@ print(f'{n_structures} remaining cells')
 
 
 #=====================================================================
-# Deleting temporary directory of POSCAR files =======================
+# Deleting temporary subdirectories of POSCAR files ==================
 #=====================================================================
 number = 0
 #--------------------------
@@ -1845,114 +1846,125 @@ for i in range(len(files0)):
 
 #=====================================================================
 # Filtering/Excluding Similar POSCAR Files ===========================
+# within the final directory of the POSCAR files =====================
 #=====================================================================
 
-n += 1
-#----------
-print(f' ')
-print(f'========================================')
-print(f'Step {n}: Deleting Similar Lattices ====')
-print(f'========================================')
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+# Introduzir o loop de exclusão, até que duas interações retornem exclusão nula
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-files = os.listdir(diret2)
-n_exclusion = 0
+n_exclusion_cont = 0
 
-for i in range(len(files)):
-    #---------------------------------
-    print(f'Progress {i+1}/{len(files)}') 
-    #----------------
-    files_delete = []
-    #------------------------------------
-    if os.path.exists(diret2 + files[i]):
-       #---------------------------------------------------------
-       structure1 = Poscar.from_file(diret2 + files[i]).structure
-       #---------------------------------------------------------
-       poscar = open(diret2 + files[i], "r")
-       #--------------------------------
-       VTemp = poscar.readline().split()
-       if (n_Lattice == 2):
-          Angle_AB1 = float(VTemp[27])
-       if (n_Lattice == 3):
-          temp_angle = VTemp[28].replace('_',' ').split()
-          Angle_AB1 = float(temp_angle[0]) 
-       #---------------------------------------------- 
-       param = poscar.readline(); param = float(param)
-       VTemp = poscar.readline().split();  Ax = float(VTemp[0])*param; Ay = float(VTemp[1])*param;  A = np.array([Ax, Ay]);  mA = np.linalg.norm(A)
-       VTemp = poscar.readline().split();  Bx = float(VTemp[0])*param; By = float(VTemp[1])*param;  B = np.array([Bx, By]);  mB = np.linalg.norm(B)
-       dAB1 = abs(mA - mB)
-       poscar.close()
-       #-------------
-
-       for j in range(len(files)):
-           if (i != j):
-              #------------------------------------
-              if os.path.exists(diret2 + files[j]):
-                 #---------------------------------------------------------
-                 structure2 = Poscar.from_file(diret2 + files[j]).structure
-                 #----------------------------------------------------------------------------------
-                 matcher = StructureMatcher()                   # Creating a StructureMatcher object
-                 if matcher.fit(structure1, structure2):        # Checking if the structures are similar
-                    #-----------------------------------------------------------------------------------
-                    poscar = open(diret2 + files[j], "r")
-                    #--------------------------------
-                    VTemp = poscar.readline().split()
-                    if (n_Lattice == 2):
-                       Angle_AB2 = float(VTemp[27])
-                    if (n_Lattice == 3):
-                       temp_angle = VTemp[28].replace('_',' ').split()
-                       Angle_AB2 = float(temp_angle[0]) 
-                    #----------------------------------------------
-                    param = poscar.readline(); param = float(param)
-                    VTemp = poscar.readline().split();  Ax = float(VTemp[0])*param; Ay = float(VTemp[1])*param;  A = np.array([Ax, Ay]);  mA = np.linalg.norm(A)
-                    VTemp = poscar.readline().split();  Bx = float(VTemp[0])*param; By = float(VTemp[1])*param;  B = np.array([Bx, By]);  mB = np.linalg.norm(B)
-                    dAB2 = abs(mA - mB)
-                    poscar.close()
-                    #----------------
-                    if (dAB1 < dAB2):
-                       if os.path.exists(diret2 + + files[j]):
-                          os.remove(diret2 + files[j])
-                          n_exclusion += 1
-                    #----------------
-                    if (dAB1 > dAB2):
-                       if os.path.exists(diret2 + files[i]):
-                          os.remove(diret2 + files[i])
-                          n_exclusion += 1
-                    #-----------------
-                    if (dAB1 == dAB2):
-                       cont = 1
-                       #--------------------------------------------------------
-                       if ( (Angle_AB1 < 0) and (Angle_AB2 > 0) and cont == 1 ):
-                          if os.path.exists(diret2 + files[i]):
-                             os.remove(diret2 + files[i])
-                             n_exclusion += 1; cont = 0
-                       if ( (Angle_AB1 > 0) and (Angle_AB2 < 0) and cont == 1 ):
-                          if os.path.exists(diret2 + files[j]):
-                             os.remove(diret2 + files[j])
-                             n_exclusion += 1; cont = 0
-                       if (abs(Angle_AB1) < abs(Angle_AB2) and cont == 1):
-                          if os.path.exists(diret2 + files[j]):
+while n_exclusion_cont != 2:
+
+   n += 1
+   #----------
+   print(f' ')
+   print(f'========================================')
+   print(f'Step {n}: Deleting Similar Lattices ====')
+   print(f'========================================')
+
+   files = os.listdir(diret2)
+   n_exclusion = 0
+
+   for i in range(len(files)):
+       #---------------------------------
+       print(f'Progress {i+1}/{len(files)}') 
+       #----------------
+       files_delete = []
+       #------------------------------------
+       if os.path.exists(diret2 + files[i]):
+          #---------------------------------------------------------
+          structure1 = Poscar.from_file(diret2 + files[i]).structure
+          #---------------------------------------------------------
+          poscar = open(diret2 + files[i], "r")
+          #--------------------------------
+          VTemp = poscar.readline().split()
+          if (n_Lattice == 2):
+             Angle_AB1 = float(VTemp[27])
+          if (n_Lattice == 3):
+             temp_angle = VTemp[28].replace('_',' ').split()
+             Angle_AB1 = float(temp_angle[0]) 
+          #---------------------------------------------- 
+          param = poscar.readline(); param = float(param)
+          VTemp = poscar.readline().split();  Ax = float(VTemp[0])*param; Ay = float(VTemp[1])*param;  A = np.array([Ax, Ay]);  mA = np.linalg.norm(A)
+          VTemp = poscar.readline().split();  Bx = float(VTemp[0])*param; By = float(VTemp[1])*param;  B = np.array([Bx, By]);  mB = np.linalg.norm(B)
+          dAB1 = abs(mA - mB)
+          poscar.close()
+          #-------------
+          for j in range(len(files)):
+              if (i != j):
+                 #------------------------------------
+                 if os.path.exists(diret2 + files[j]):
+                    #---------------------------------------------------------
+                    structure2 = Poscar.from_file(diret2 + files[j]).structure
+                    #----------------------------------------------------------------------------------
+                    matcher = StructureMatcher()                   # Creating a StructureMatcher object
+                    if matcher.fit(structure1, structure2):        # Checking if the structures are similar
+                       #-----------------------------------------------------------------------------------
+                       poscar = open(diret2 + files[j], "r")
+                       #--------------------------------
+                       VTemp = poscar.readline().split()
+                       if (n_Lattice == 2):
+                          Angle_AB2 = float(VTemp[27])
+                       if (n_Lattice == 3):
+                          temp_angle = VTemp[28].replace('_',' ').split()
+                          Angle_AB2 = float(temp_angle[0]) 
+                       #----------------------------------------------
+                       param = poscar.readline(); param = float(param)
+                       VTemp = poscar.readline().split();  Ax = float(VTemp[0])*param; Ay = float(VTemp[1])*param;  A = np.array([Ax, Ay]);  mA = np.linalg.norm(A)
+                       VTemp = poscar.readline().split();  Bx = float(VTemp[0])*param; By = float(VTemp[1])*param;  B = np.array([Bx, By]);  mB = np.linalg.norm(B)
+                       dAB2 = abs(mA - mB)
+                       poscar.close()
+                       #----------------
+                       if (dAB1 < dAB2):
+                          if os.path.exists(diret2 + + files[j]):
                              os.remove(diret2 + files[j])
-                             n_exclusion += 1; cont = 0
-                       if (abs(Angle_AB1) > abs(Angle_AB2) and cont == 1):
+                             n_exclusion += 1
+                       #----------------
+                       if (dAB1 > dAB2):
                           if os.path.exists(diret2 + files[i]):
                              os.remove(diret2 + files[i])
-                             n_exclusion += 1; cont = 0
-                       if (Angle_AB1 == Angle_AB2 and cont == 1):
-                          if os.path.exists(diret2 + files[j]):
-                             os.remove(diret2 + files[j])
                              n_exclusion += 1
-
-#-------------------------
-files = os.listdir(diret2)
-n_structures = len(files)
-#------------------------
-
-print(f'============================================')
-print(f'{n_exclusion} cells were filtered/excluded')
-print(f'--------------------------------------------')
-if (n_structures == 1): print(f'Only one cell was found')
-if (n_structures >  1): print(f'{n_structures} cells were found')
-print(f'============================================')
+                       #-----------------
+                       if (dAB1 == dAB2):
+                          cont = 1
+                          #--------------------------------------------------------
+                          if ( (Angle_AB1 < 0) and (Angle_AB2 > 0) and cont == 1 ):
+                             if os.path.exists(diret2 + files[i]):
+                                os.remove(diret2 + files[i])
+                                n_exclusion += 1; cont = 0
+                          if ( (Angle_AB1 > 0) and (Angle_AB2 < 0) and cont == 1 ):
+                             if os.path.exists(diret2 + files[j]):
+                                os.remove(diret2 + files[j])
+                                n_exclusion += 1; cont = 0
+                          if (abs(Angle_AB1) < abs(Angle_AB2) and cont == 1):
+                             if os.path.exists(diret2 + files[j]):
+                                os.remove(diret2 + files[j])
+                                n_exclusion += 1; cont = 0
+                          if (abs(Angle_AB1) > abs(Angle_AB2) and cont == 1):
+                             if os.path.exists(diret2 + files[i]):
+                                os.remove(diret2 + files[i])
+                                n_exclusion += 1; cont = 0
+                          if (Angle_AB1 == Angle_AB2 and cont == 1):
+                             if os.path.exists(diret2 + files[j]):
+                                os.remove(diret2 + files[j])
+                                n_exclusion += 1
+   #-------------------------
+   files = os.listdir(diret2)
+   n_structures = len(files)
+   #------------------------
+
+   print(f'============================================')
+   print(f'{n_exclusion} cells were filtered/excluded')
+   print(f'--------------------------------------------')
+   if (n_structures == 1): print(f'Only one cell was found')
+   if (n_structures >  1): print(f'{n_structures} cells were found')
+   print(f'============================================')
+
+   if (n_exclusion != 0):  n_exclusion_cont  = 0
+   if (n_exclusion == 0):  n_exclusion_cont += 1
+   if (n_structures == 1): n_exclusion_cont  = 2
 
 
 #=====================================================================

samba_ilum-1.0.0.542/samba_ilum/src/energy_scan.py

@@ -0,0 +1,57 @@
+# SAMBA_ilum Copyright (C) 2025 - Closed source
+
+
+import os
+
+
+try:
+    path_dir, name_dir = os.path.split(os.getcwd())
+except Exception as e:
+    pass
+
+
+#----------------
+converged = False
+#----------------
+try:
+    with open('OUTCAR', 'r') as f:
+        for line in f:
+            if 'reached' in line:
+                converged = True
+                break
+except FileNotFoundError:
+    pass
+except Exception as e:
+    pass
+
+
+if converged:
+    try:
+        with open('OSZICAR', 'r') as f:
+            last_line = f.readlines()[-1].strip()
+            energy_value = last_line.replace('=', ' ').split()[4]
+        #--------------------------------------------------------
+        with open('../energy_scan.txt', "a") as energy_file:
+            energy_file.write(f'{name_dir} {energy_value}\n')
+            #---------------------------------------------
+            temp_name = name_dir.replace('_', ' ').split()
+            #---------------------------------------------
+            if len(temp_name) == 2:
+                t_temp_name_original = temp_name.copy()
+                #---------------------------------------------
+                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 = f'{temp_name[0]}_{temp_name[1]}'
+                    energy_file.write(f'{new_name_dir} {energy_value}\n')
+                #------------------------------------------------------------------------
+                if t_temp_name_original[0] == '0.0' and t_temp_name_original[1] == '0.0':
+                    energy_file.write(f'1.0_0.0 {energy_value}\n')
+                    energy_file.write(f'0.0_1.0 {energy_value}\n')
+    except FileNotFoundError:
+        pass
+    except IndexError:
+        pass
+    except Exception as e:
+        pass

{samba_ilum-1.0.0.540 → samba_ilum-1.0.0.542}/samba_ilum/src/job.py

@@ -130,8 +130,8 @@ job.write(f'                         $vasp_std || echo "Error in VASP in $dir0/$
 job.write(f'                         sleep 10 \n')
 job.write(f'                         python3 contcar_update.py \n')
 job.write(f'                         python3 energy_scan.py \n')
-job.write(f'                         rm -r CHG CHGCAR DOSCAR PROCAR WAVECAR INCAR KPOINTS OSZICAR PCDAT POTCAR REPORT XDATCAR vdw_kernel.bindat EIGENVAL IBZKPT vasprun.xml *.py \n')
-job.write(f'                         bzip2 OUTCAR \n')
+job.write(f'                         rm -r CHG CHGCAR DOSCAR PROCAR WAVECAR INCAR KPOINTS PCDAT POTCAR REPORT XDATCAR vdw_kernel.bindat EIGENVAL IBZKPT vasprun.xml *.py \n')
+job.write(f'                         bzip2 OUTCAR OSZICAR \n')
 job.write(f'                     done \n')
 job.write(f'                     #------------- \n')
 job.write(f'                     cd $dir0/$i/$j \n')
@@ -174,8 +174,8 @@ job.write(f'                                $vasp_std || echo "Error in VASP in
 job.write(f'                                sleep 10 \n')
 job.write(f'                                python3 contcar_update.py \n')
 job.write(f'                                python3 energy_scan.py \n')
-job.write(f'                                rm -r CHG CHGCAR DOSCAR PROCAR WAVECAR INCAR KPOINTS OSZICAR PCDAT POTCAR REPORT XDATCAR vdw_kernel.bindat EIGENVAL IBZKPT vasprun.xml *.py \n')
-job.write(f'                                bzip2 OUTCAR \n')
+job.write(f'                                rm -r CHG CHGCAR DOSCAR PROCAR WAVECAR INCAR KPOINTS PCDAT POTCAR REPORT XDATCAR vdw_kernel.bindat EIGENVAL IBZKPT vasprun.xml *.py \n')
+job.write(f'                                bzip2 OUTCAR OSZICAR \n')
 job.write(f'                                cd $dir0/$i/$j \n')
 job.write(f'                                mv $k OK_$k \n')
 job.write(f'                             fi \n')

{samba_ilum-1.0.0.540 → samba_ilum-1.0.0.542}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.540",
+    version = "1.0.0.542",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo", 

samba_ilum-1.0.0.540/samba_ilum/src/energy_scan.py

@@ -1,35 +0,0 @@
-# SAMBA_ilum Copyright (C) 2025 - Closed source
-
-
-import os
-
-#===================================================
-# Getting the path and name of the current directory:
-path_dir, name_dir = os.path.split(os.getcwd())
-#===============================================
-
-if os.path.isfile('../energy_scan.txt'):  energy = open('../energy_scan.txt', "a")
-else:  energy = open('../energy_scan.txt', "w")
-
-with open('OSZICAR') as file:
-    lines = file.readlines()
-VTemp = lines[-1].strip()
-
-energia = VTemp.replace('=',' ').split()
-
-energy.write(f'{name_dir} {energia[4]} \n')
-
-temp_name = name_dir.replace('_', ' ').split()
-t_temp_name = temp_name
-#------------------------
-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')
-   if (t_temp_name[0] == '1.0' and t_temp_name[1] == '1.0'):
-      energy.write(f'1.0_0.0 {energia[4]} \n')
-      energy.write(f'0.0_1.0 {energia[4]} \n')
-
-energy.close()