SAMBA-ilum 1.0.0.531__tar.gz → 1.0.0.533__tar.gz

{samba_ilum-1.0.0.531 → samba_ilum-1.0.0.533}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.531
+Version: 1.0.0.533
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.531 → samba_ilum-1.0.0.533}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.531
+Version: 1.0.0.533
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.531 → samba_ilum-1.0.0.533}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.531'
+version = '1.0.0.533'
 
 print(" ")
 print("=============================================================")

{samba_ilum-1.0.0.531 → samba_ilum-1.0.0.533}/samba_ilum/src/HeteroStructure_Generator.py

@@ -1976,19 +1976,18 @@ for i in range(len(files)):
     VTemp1 = VTemp[-1].split()
     #-------------------------
     pulo = n_Lattice +4 
-    tag1_str  = VTemp[pulo + 1];   tag1  = [float(x) for x in tag1_str.split('_')]    # mismatch_areas_12_21
-    tag2_str  = VTemp[pulo + 5];   tag2  = [float(x) for x in tag2_str.split('_')]    # var_areas
-    tag3_str  = VTemp[pulo + 9];   tag3  = [float(x) for x in tag3_str.split('_')]    # var_vectors
-    tag4_str  = VTemp[pulo + 13];  tag4  = [float(x) for x in tag4_str.split('_')]    # mismatch_angles_12_21
-    tag5_str  = VTemp[pulo + 17];  tag5  = [float(x) for x in tag5_str.split('_')]    # var_angles
-    tag6_str  = VTemp[pulo + 21];  tag6  = [float(x) for x in tag6_str.split('_')]    # rotation_angle
-    tag7_str  = VTemp[pulo + 25];  tag7  = [float(x) for x in tag7_str.split('_')]    # MSCell_1
-    tag8_str  = VTemp[pulo + 29];  tag8  = [float(x) for x in tag8_str.split('_')]    # MSCell_2
-    tag9_str  = VTemp[pulo + 33];  tag9  = [float(x) for x in tag9_str.split('_')]    # MDeform_1
-    tag10_str = VTemp[pulo + 37];  tag10 = [float(x) for x in tag10_str.split('_')]   # MDeform_2
-    #--------------------------------------------------------------------------------------------
-    data_hash = [tag1, tag2, tag3, tag4, tag5, tag6, tag7, tag8, tag9, tag10]
-    #------------------------------------------------------------------------
+    tag1_str = VTemp[pulo + 1];   tag1 = [float(x) for x in tag1_str.split('_')]   # mismatch_areas_12_21
+    tag2_str = VTemp[pulo + 5];   tag2 = [float(x) for x in tag2_str.split('_')]   # var_areas
+    tag3_str = VTemp[pulo + 9];   tag3 = [float(x) for x in tag3_str.split('_')]   # var_vectors
+    tag4_str = VTemp[pulo + 13];  tag4 = [float(x) for x in tag4_str.split('_')]   # mismatch_angles_12_21
+    tag5_str = VTemp[pulo + 17];  tag5 = [float(x) for x in tag5_str.split('_')]   # var_angles
+    tag6_str = VTemp[pulo + 25];  tag6 = [float(x) for x in tag6_str.split('_')]   # MSCell_1
+    tag7_str = VTemp[pulo + 29];  tag7 = [float(x) for x in tag7_str.split('_')]   # MSCell_2
+    tag8_str = VTemp[pulo + 33];  tag8 = [float(x) for x in tag8_str.split('_')]   # MDeform_1
+    tag9_str = VTemp[pulo + 37];  tag9 = [float(x) for x in tag9_str.split('_')]   # MDeform_2
+    #-----------------------------------------------------------------------------------------
+    data_hash = [tag1, tag2, tag3, tag4, tag5, tag6, tag7, tag8, tag9]
+    #-----------------------------------------------------------------
     new_id = hashlib.sha1(json.dumps(data_hash, separators=(',', ':')).encode('utf-8')).hexdigest()[:8]
     #--------------------------------------------------------------------------------------------------
 

{samba_ilum-1.0.0.531 → samba_ilum-1.0.0.533}/samba_ilum/src/cell_check.py

@@ -16,6 +16,8 @@ import numpy as np
 import shutil
 import glob
 import uuid
+import hashlib
+import json
 import sys
 import os
 
@@ -41,62 +43,6 @@ files0 = [name for name in os.listdir(poscar_dir_path) if os.path.isfile(os.path
 
 
 
-#============================================
-# creating IDs for POSCAR files =============
-#============================================
-id_poscar_files = open(dir_files + '/ID_POSCAR_Files.txt', 'w')
-#---------------------------
-for i in range(len(files0)):
-    #--------------------------------------------
-    Lattice0 = dir_files + '/' + dir_poscar + '/'
-    poscar = open(Lattice0 + files0[i], 'r')
-    VTemp1 = poscar.readline().split()
-    for j in range(4): VTemp = poscar.readline()
-    VTemp2 = poscar.readline().split()
-    VTemp3 = poscar.readline().split()
-    poscar.close()
-    #-------------
-    temp_ion = ''
-    temp_nion = 0
-    for j in range(len(VTemp2)):
-        temp_ion += str(VTemp2[j]) 
-        temp_nion += int(VTemp3[j])
-        if (j < (len(VTemp2) -1)):
-           temp_ion += '_' 
-    #-------------------------
-    if (VTemp1[0] != 'SAMBA'):
-       #----------------------
-       id_material = ''
-       unique_id = str(uuid.uuid4().hex[:16])
-       #---------------------------------------
-       poscar = open(Lattice0 + files0[i], "r")
-       for j in range(5): VTemp = poscar.readline()
-       VTemp3 = poscar.readline().split()
-       VTemp4 = poscar.readline().split()
-       poscar.close()
-       #---------------------------
-       for j in range(len(VTemp3)):
-           id_material += str(VTemp3[j])
-           if (str(VTemp4[j]) != '1'): id_material += str(VTemp4[j])
-       id_material +=  '_' + unique_id
-       #--------------------------------------------------------------------
-       with open(Lattice0 + files0[i], 'r') as file: line = file.readlines()
-       line[0] = 'SAMBA ' + temp_ion + ' ' + str(temp_nion) + ' ' + id_material + '\n'
-       with open(Lattice0 + files0[i], 'w') as file: file.writelines(line)
-       #------------------------------------------------------------------
-       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
-    #-------------------------
-    if (VTemp1[0] == 'SAMBA'):
-       #----------------------------
-       id_material = str(VTemp1[-1])
-       #--------------------------------------------------------
-       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
-#----------------------
-id_poscar_files.close()
-if (os.path.getsize(dir_files + '/ID_POSCAR_Files.txt') == 0): os.remove(dir_files + '/ID_POSCAR_Files.txt')
-#-----------------------------------------------------------------------------------------------------------
-
-
 #============================================
 # Testing POSCAR file compatibility =========
 #============================================
@@ -303,3 +249,84 @@ for name in files0:
         if (axis_correction > 0): sys.exit()
 
 delete_hidden_files(poscar_dir_path)
+
+
+
+#============================================
+# creating IDs for POSCAR files =============
+#============================================
+id_poscar_files = open(dir_files + '/ID_POSCAR_Files.txt', 'w')
+for i in range(len(files0)):
+    #--------------------------------------------
+    Lattice0 = dir_files + '/' + dir_poscar + '/'
+    poscar = open(Lattice0 + files0[i], 'r')
+    VTemp1 = poscar.readline().split()
+    for j in range(4): VTemp = poscar.readline()
+    VTemp2 = poscar.readline().split()
+    VTemp3 = poscar.readline().split()
+    poscar.close()
+    #-------------
+    temp_ion = ''
+    temp_nion = 0
+    for j in range(len(VTemp2)):
+        temp_ion += str(VTemp2[j]) 
+        temp_nion += int(VTemp3[j])
+        if (j < (len(VTemp2) -1)): temp_ion += '_' 
+    #---------------------------------------------
+    if (VTemp1[0] != 'SAMBA'):
+       #----------------------
+       id_material = ''
+       #---------------------------------------
+       poscar = open(Lattice0 + files0[i], "r")
+       for j in range(5): VTemp = poscar.readline()
+       VTemp3 = poscar.readline().split()
+       VTemp4 = poscar.readline().split()
+       poscar.close()
+       #--------------------------------------------------------------------------------------------
+       # Creating a unique 16-digit ID that encodes the POSCAR file structure ----------------------
+       #--------------------------------------------------------------------------------------------
+       with open(poscar, 'r') as f: lines = [line.strip() for line in f.readlines() if line.strip()]
+       #-----------------------
+       tag_1 = float(lines[1])
+       #---------
+       tag_2 = []
+       for i in range(2, 5):
+           vector = [float(x) for x in lines[i].split()]
+           tag_2.append(vector)
+       #-----------------------
+       tag_3 = lines[5].split()
+       #-----------------------
+       tag_4 = [int(x) for x in lines[6].split()]
+       #-----------------------------------------
+       tag_5 = lines[7].lower()
+       #-----------------------
+       tag_6 = []
+       natoms = sum(tag_4)
+       for i in range(8, 8 + natoms):
+           coord = [float(x) for x in lines[i].split()]
+           tag_6.append(coord)
+       #----------------------
+       data_hash = [tag_1, tag_2, tag_3, tag_4, tag_5, tag_6]
+       canonical_string = json.dumps(data_hash, separators=(',', ':'))
+       unique_id = hashlib.sha256(canonical_string.encode('utf-8')).hexdigest()[:16]
+       #-------------------------------------------------------------------------
+       for j in range(len(VTemp3)):
+           id_material += str(VTemp3[j])
+           if (str(VTemp4[j]) != '1'): id_material += str(VTemp4[j])
+       id_material +=  '_' + unique_id
+       #--------------------------------------------------------------------
+       with open(Lattice0 + files0[i], 'r') as file: line = file.readlines()
+       line[0] = 'SAMBA ' + temp_ion + ' ' + str(temp_nion) + ' ' + id_material + '\n'
+       with open(Lattice0 + files0[i], 'w') as file: file.writelines(line)
+       #------------------------------------------------------------------
+       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
+    #-------------------------
+    if (VTemp1[0] == 'SAMBA'):
+       #----------------------------
+       id_material = str(VTemp1[-1])
+       #--------------------------------------------------------
+       id_poscar_files.write(f'{files0[i]} >> {id_material} \n')
+#----------------------
+id_poscar_files.close()
+#----------------------
+

{samba_ilum-1.0.0.531 → samba_ilum-1.0.0.533}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.531",
+    version = "1.0.0.533",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",