SAMBA-ilum 1.1.0.116__tar.gz → 1.1.0.117__tar.gz

{samba_ilum-1.1.0.116 → samba_ilum-1.1.0.117}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.1.0.116
+Version: 1.1.0.117
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.1.0.116 → samba_ilum-1.1.0.117}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.1.0.116
+Version: 1.1.0.117
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

samba_ilum-1.1.0.117/SAMBA_ilum.egg-info/SOURCES.txt

@@ -0,0 +1,40 @@
+LICENSE.txt
+README.md
+setup.cfg
+setup.py
+SAMBA_ilum.egg-info/PKG-INFO
+SAMBA_ilum.egg-info/SOURCES.txt
+SAMBA_ilum.egg-info/dependency_links.txt
+SAMBA_ilum.egg-info/entry_points.txt
+SAMBA_ilum.egg-info/requires.txt
+SAMBA_ilum.egg-info/top_level.txt
+samba_ilum/__init__.py
+samba_ilum/__main__.py
+samba_ilum/src/BZ_2D.py
+samba_ilum/src/HeteroStructure_Generator.py
+samba_ilum/src/_info_pseudo.py
+samba_ilum/src/a-scan.py
+samba_ilum/src/a-scan_analysis.py
+samba_ilum/src/bader_poscar.py
+samba_ilum/src/bader_update.py
+samba_ilum/src/cell_check.py
+samba_ilum/src/charge_transfer.py
+samba_ilum/src/contcar_update.py
+samba_ilum/src/data-base_json.py
+samba_ilum/src/data-base_union.py
+samba_ilum/src/energy_scan.py
+samba_ilum/src/hubbard_correction.py
+samba_ilum/src/job.py
+samba_ilum/src/kpoints.py
+samba_ilum/src/lattice_plot3d.py
+samba_ilum/src/make_files.py
+samba_ilum/src/output.py
+samba_ilum/src/poscar_fix_direct_coord.py
+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.py
+samba_ilum/src/xyz-scan_analysis.py
+samba_ilum/src/z-scan.py
+samba_ilum/src/z-scan_analysis.py

samba_ilum-1.1.0.117/SAMBA_ilum.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+samba_ilum = samba_ilum.__main__:main

samba_ilum-1.1.0.117/samba_ilum/__main__.py

@@ -0,0 +1,317 @@
+# SAMBA_ilum Copyright (C) 2025 - Closed source
+
+def main():
+    import numpy as np
+    import subprocess
+    import itertools
+    import shutil
+    import time
+    import sys
+    import os
+
+    #----------------
+    dir_codes = 'src'
+    dir_files = os.getcwd()
+    os.chdir(os.path.dirname(os.path.realpath(__file__)))
+    dir_samba = os.path.dirname(os.path.realpath(__file__))
+    print(f'{dir_samba}')
+    #--------------------
+
+    version = '1.1.0.117'
+
+    print(" ")
+    print("=============================================================")
+    print(f'SAMBA_ilum v{version} Copyright (C) 2025 --------------------')
+    print("Closed source: Adalberto Fazzio's research group (Ilum|CNPEM)")
+    print("Author: Augusto de Lelis Araujo -----------------------------")
+    print("=============================================================")
+    print(" ")
+    print("   _____ ___    __  _______  ___       _ __              ")
+    print("  / ___//   |  /  |/  / __ )/   |     (_) /_  ______ ___ ")
+    print("""  \__ \/ /| | / /|_/ / __  / /| |    / / / / / / __ `___\ """)
+    print(" ___/ / ___ |/ /  / / /_/ / ___ |   / / / /_/ / / / / / /")
+    print("/____/_/  |_/_/  /_/_____/_/  |_|  /_/_/\__,_/_/ /_/ /_/ ")
+    print(f'Simulation and Automated Methods for Bilayer Analysis v{version}')
+    print(" ")
+
+    #------------------------------------------------
+    # Checking for updates for SAMBA ----------------
+    #------------------------------------------------
+    try:
+        url = f"https://pypi.org/pypi/{'samba_ilum'}/json"
+        response = requests.get(url)
+        dados = response.json()
+        current_version = dados['info']['version']; current_version = str(current_version)
+        if (current_version != version):
+           print(" ")
+           print("--------------------------------------------------------------")
+           print("        !!!!! Your SAMBA version is out of date !!!!!         ")
+           print("--------------------------------------------------------------")
+           print("    To update, close the SAMBA and enter into the terminal:   ")
+           print("                 pip install --upgrade samba                  ")
+           print("--------------------------------------------------------------")
+           print(" ")
+           print(" ")
+        ...
+    except Exception as e:
+        print("--------------------------------------------------------------")
+        print("    !!!! Unable to verify the current version of SAMBA !!!!   ")
+        print("--------------------------------------------------------------")
+        print(" ")
+
+
+    # ------------------------------------------------------------------------------
+    # Checking if the "run.input" file exists --------------------------------------
+    # ------------------------------------------------------------------------------
+    run_input = 'not'
+    #----------------
+    if os.path.isfile(dir_files + '/run.input'): run_input = 'yes'
+    else: run_input = 'not'
+    # ----------------------
+    if (run_input == 'yes'):
+       run = open(dir_files + '/run.input', "r")
+       VTemp = run.readline().split()
+       if (len(VTemp) == 3): tarefa = int(VTemp[2])
+
+
+    if(run_input == 'not'):
+       print("######################################################################")
+       print("# What do you want to run? ===========================================")
+       print("# ====================================================================")
+       print("# [0] Generate SAMBA execution inputs                                 ")
+       print("# --------------------------------------------------------------------")
+       print("# [1] Heterostructure Generator                                       ")
+       print("# [2] WorkFlow: High Throughput DFT (inputs + job)                    ")
+       print("# --------------------------------------------------------------------")
+       print("# [3] Customize internal WorkFlow inputs (INPUTS folder)              ")
+       print("######################################################################")
+       print("A tutorial on how to use the SAMBA is available on GitHub at the link:")
+       print("https://github.com/Augusto-de-Lelis-Araujo/SAMBA/blob/main/README.md  ")
+       print("######################################################################")
+       tarefa = input(" "); tarefa = int(tarefa)
+       print(" ")
+
+
+    if (tarefa == 0):
+       shutil.copyfile(dir_codes + '/INPUTS/SAMBA_WorkFlow.input', dir_files + '/SAMBA_WorkFlow.input')
+       shutil.copyfile(dir_codes + '/INPUTS/SAMBA_HeteroStructure.input', dir_files + '/SAMBA_HeteroStructure.input')
+
+
+    if (tarefa == 1):
+       #--------------------------------------------------------------------------------------------------
+       # Checking if the "SAMBA_HeteroStructure.input" file exists, if it does not exist it is created ---
+       #--------------------------------------------------------------------------------------------------
+       if os.path.isfile(dir_files + '/SAMBA_HeteroStructure.input'):
+          0 == 0
+       else:
+          shutil.copyfile(dir_codes + '/SAMBA_HeteroStructure.input', dir_files + '/SAMBA_HeteroStructure.input')
+          #------------------------------------------------------------------------------------------------------
+          print(" ")
+          print("==============================================================")
+          print("Generated SAMBA_HeteroStructure.input file !!! ===============")
+          print("--------------------------------------------------------------")
+          print("Configure the SAMBA_HeteroStructure.input file and run the ---")
+          print("                                                code again ---")
+          print("==============================================================")
+          print(" ")
+          #--------------------------------------------------------
+          confirmacao = input (" "); confirmacao = str(confirmacao)
+          sys.exit()
+          #---------
+
+       #------------------------------------------------------------
+       exec(open(dir_files + '/SAMBA_HeteroStructure.input').read())
+       #------------------------------------------------------------
+       separacao1 = separation_1
+       separacao2 = separation_2
+       #------------------------
+       if (loop_ht == 0):
+          Lattice1 = Lattice1.replace(".vasp","") + ".vasp"
+          Lattice2 = Lattice2.replace(".vasp","") + ".vasp"
+          Lattice3 = Lattice3.replace(".vasp","") + ".vasp"
+       #---------------------------------------------------
+
+       #=============================================================
+       # Fixing the coordinates of POSCAR files in direct form ======
+       #=============================================================
+       dir_files_in = dir_poscar
+       exec(open(dir_codes + '/poscar_fix_direct_coord.py').read())
+       #=============================================================
+       # Checking the structure of POSCAR files, regarding the ======
+       # rotation angle in relation to the z-axis ===================
+       #=============================================================
+       exec(open(dir_codes + '/cell_check.py').read())
+       #=============================================================
+
+       if (loop_ht == 1):
+          #--------------
+          n_Lattice = 2
+          #--------------------------------------------------------------------------
+          # Checking for existence of non-empty file 'check_list_loop.txt' ----------
+          #--------------------------------------------------------------------------
+          temp_check = 0
+          #-------------
+          check_list_dir = dir_files + '/check_list_loop.txt'
+          if os.path.exists(check_list_dir) and os.path.getsize(check_list_dir) != 0:
+             check = np.loadtxt(check_list_dir, dtype='str');  check.shape
+             n_ht = check[:,0];  mat1 = check[:,1];  mat2 = check[:,2]
+             temp_check = 1
+          #------------------------------
+          if (temp_check == 0): nloop = 0
+          if (temp_check == 1): nloop = len(mat1)
+          #--------------------------------------
+          temp_dir = dir_files + '/' + dir_poscar
+          files0 = [name for name in os.listdir(temp_dir) if os.path.isfile(os.path.join(temp_dir, name))]  # Listando os arquivos dentro do diretório "dir_poscar"
+          files = sorted(files0)
+          #---------------------------------------------------------------------
+          # bilayer_materials = list(itertools.combinations(files, 2))
+          # for material in files:  bilayer_materials.append((material, material))
+          #---------------------------------------------------------------------
+          bilayer_materials = []
+          for material1 in files:
+              for material2 in files:
+                  bilayer_materials.append((material1, material2))
+          #-------------------------------------------------------
+          vistos = set()
+          new_bilayer_materials = []                      # List to store unique elements
+          for elemento in bilayer_materials:
+              elem_ordenado = tuple(sorted(elemento))     # Sorts the elements (ignoring permutations)
+              if elem_ordenado not in vistos:
+                  new_bilayer_materials.append(elemento)  # Adding elements that do not have permutations
+                  vistos.add(elem_ordenado)
+          bilayer_materials = new_bilayer_materials       # Saving the new list with the permutations removed
+          #-------------------------------------------------------
+          for loop in range(len(bilayer_materials)):
+              Lattice1 = bilayer_materials[loop][0]
+              Lattice2 = bilayer_materials[loop][1]
+              Lattice3 = ''
+              #------
+              run = 1
+              #-------------------
+              if (temp_check == 1):
+                 for mnt in range(len(mat1)):
+                     temp0_mat1 = str(mat1[mnt]); temp0_mat2 = str(mat2[mnt])
+                     temp1_mat1 = Lattice1.replace('.vasp', ''); temp1_mat2 = Lattice2.replace('.vasp', '')
+                     if ( (temp0_mat1 == temp1_mat1 and temp0_mat2 == temp1_mat2) or (temp0_mat1 == temp1_mat2 and temp0_mat2 == temp1_mat1) ): run = 0
+                     #---------------------------------------------------------------------------------------------------------------------------------
+
+              if ( temp_check == 0 or (temp_check == 1 and run == 1) ):
+                 #------------------------------------------------------------------
+                 # Heterostructure loop check_list ---------------------------------
+                 #------------------------------------------------------------------
+                 nloop += +1
+                 if (nloop >= 0    and nloop < 10):   nloop2 = '000' + str(nloop)
+                 if (nloop >= 10   and nloop < 100):  nloop2 = '00'  + str(nloop)
+                 if (nloop >= 100  and nloop < 1000): nloop2 = '0'   + str(nloop)
+                 if (nloop >  1000):                  nloop2 =         str(nloop)
+                 dir_loop = str(nloop2) + '--' + Lattice1.replace('.vasp', '') + '--' + Lattice2.replace('.vasp', '')
+                 #---------------------------------------------------------------------------------------------------
+                 check_list = open(dir_files + '/check_list_loop.txt', 'a')
+                 t_Lattice1 = Lattice1.replace('.vasp', ' ');  t_Lattice2 = Lattice2.replace('.vasp', ' ')
+                 if (n_Lattice == 2):
+                    check_list.write(f'{nloop2} {t_Lattice1} {t_Lattice2} \n')
+                 if (n_Lattice == 3):
+                    t_Lattice3 = Lattice3.replace('.vasp', ' ')
+                    check_list.write(f'{nloop2} {t_Lattice1} {t_Lattice2} {t_Lattice3} \n')
+                 check_list.close()
+                 #-----------------
+
+                 try:
+                     exec(open(dir_codes + '/HeteroStructure_Generator.py').read())
+                     ...
+                 except SystemExit as e: 0 == 0
+                 except Exception as e: 0 == 0
+                 #----------------------------
+
+       if (loop_ht == 0): exec(open(dir_codes + '/HeteroStructure_Generator.py').read())
+
+
+    if (tarefa == 2):
+       #-------------------------------------------------------------------------------------------
+       # Checking if the "SAMBA_WorkFlow.input" file exists, if it does not exist it is created ---
+       #-------------------------------------------------------------------------------------------
+       if os.path.isfile(dir_files + '/SAMBA_WorkFlow.input'):
+          0 == 0
+       else:
+          shutil.copyfile(dir_codes + '/SAMBA_WorkFlow.input', dir_files + '/SAMBA_WorkFlow.input')
+          #----------------------------------------------------------------------------------------
+          print(" ")
+          print("==============================================================")
+          print("SAMBA_WorkFlow.input file generated !!! ======================")
+          print("--------------------------------------------------------------")
+          print("Configure the SAMBA_WorkFlow.input file and run the code again")
+          print("==============================================================")
+          print(" ")
+          #--------------------------------------------------------
+          confirmacao = input (" "); confirmacao = str(confirmacao)
+          sys.exit()
+          #---------
+
+       #----------------------------------------------------
+       # Checking if the "WorkFlow_INPUTS" folder exists ---
+       #----------------------------------------------------
+       if os.path.isdir(dir_files + '/WorkFlow_INPUTS'):
+          dir_inputs = dir_files + '/WorkFlow_INPUTS'
+       else:
+          dir_inputs = dir_codes + '/INPUTS'
+       #------------------------------------------------------
+       dir_inputs_vasprocar = dir_inputs + '/inputs_VASProcar'
+       #------------------------------------------------------
+
+       #------------------------------------------------
+       # Checking if the "POTCAR" folder exists --------
+       #------------------------------------------------
+       if os.path.isdir(dir_files + '/POTCAR'):
+          0 == 0
+       else:
+          print('')
+          print('Warning: -----------------------------------------')
+          print('Missing POTCAR folder and POTCAR_[ion] files -----')
+          print('Enter and then press [ENTER] to continue ---------')
+          print('--------------------------------------------------')
+          confirmacao = input (" "); confirmacao = str(confirmacao)
+       #------------------------------------
+       dir_pseudo = dir_files + '/POTCAR'
+       shutil.copyfile(dir_codes + '/_info_pseudo.py', dir_pseudo + '/_info_pseudo.py')
+       os.chdir(dir_pseudo)
+       exec(open(dir_pseudo + '/_info_pseudo.py').read())
+       os.chdir(dir_samba)
+       #------------------
+
+       #-----------------------------------------------------
+       exec(open(dir_files + '/SAMBA_WorkFlow.input').read())
+       #-----------------------------------------------------
+       vacuo = vacuum
+       #-------------
+       dir_out   = dir_files + '/' + dir_o
+       #----------------------------------
+       task = []
+       for i in range(len(tasks)):
+           if (tasks[i] == 'a-scan' or tasks[i] == 'z-scan' or tasks[i] == 'xy-scan' or tasks[i] == 'xyz-scan' or tasks[i] == 'relax'):  task.append(tasks[i])
+           for j in range(len(type)):
+               if (type[j] == 'sem_SO'):  rot = ''
+               if (type[j] == 'com_SO'):  rot = '.SO'
+               if (tasks[i] != 'a-scan' and tasks[i] != 'z-scan' and tasks[i] != 'xy-scan' and tasks[i] != 'xyz-scan' and tasks[i] != 'relax'):  task.append(tasks[i] + rot)
+       #--------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+       #=============================================================
+       # Fixing the coordinates of POSCAR files in direct form ======
+       #=============================================================
+       dir_files_in = 'Structures'
+       exec(open(dir_codes + '/poscar_fix_direct_coord.py').read())
+       #=============================================================
+       exec(open(dir_codes + '/make_files.py').read())
+       #=============================================================
+
+
+    if (tarefa == 3):  shutil.copytree(dir_codes + '/INPUTS', dir_files + '/WorkFlow_INPUTS')
+
+
+    print(" ")
+    print("=============")
+    print("Completed ===")
+    print("=============")
+    print(" ")
+
+if __name__ == '__main__':
+    main()

{samba_ilum-1.1.0.116 → samba_ilum-1.1.0.117}/setup.py

@@ -6,10 +6,14 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.1.0.116",
-    entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
+    version = "1.1.0.117",
+    # Define os pacotes a serem incluídos
+    # Isso empacotará tanto samba_ilum quanto samba_ilum.src
+    packages=['samba_ilum', 'samba_ilum.src'],
+    # A entrada principal para o comando do terminal
+    entry_points={'console_scripts': ['samba_ilum = samba_ilum.__main__:main']},
     description = "...",
-    author = "Augusto de Lelis Araujo", 
+    author = "Augusto de Lelis Araujo",
     author_email = "augusto-lelis@outlook.com",
     license = "Closed source",
     install_requires=['matplotlib',
@@ -21,7 +25,8 @@ setup(
                       'numpy',
                       'uuid',
                       'vasprocar'],
-    package_data={"": ['*.dat', '*.png', '*.jpg', '*']},
+    # Garante que os arquivos .dat, .png, etc. sejam incluídos
+    package_data={'samba_ilum': ['*.dat', '*.png', '*.jpg', '*']},
 )
 
 # python3 -m pip install --upgrade twine

samba_ilum-1.1.0.116/SAMBA_ilum.egg-info/SOURCES.txt

@@ -1,66 +0,0 @@
-LICENSE.txt
-README.md
-setup.cfg
-setup.py
-SAMBA_ilum.egg-info/PKG-INFO
-SAMBA_ilum.egg-info/SOURCES.txt
-SAMBA_ilum.egg-info/dependency_links.txt
-SAMBA_ilum.egg-info/entry_points.txt
-SAMBA_ilum.egg-info/requires.txt
-SAMBA_ilum.egg-info/top_level.txt
-samba_ilum/__init__.py
-samba_ilum/__main__.py
-samba_ilum/src/BZ_2D.py
-samba_ilum/src/HeteroStructure_Generator.py
-samba_ilum/src/_info_pseudo.py
-samba_ilum/src/a-scan.py
-samba_ilum/src/a-scan_analysis.py
-samba_ilum/src/bader
-samba_ilum/src/bader_poscar.py
-samba_ilum/src/bader_update.py
-samba_ilum/src/cell_check.py
-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_union.py
-samba_ilum/src/energy_scan.py
-samba_ilum/src/hubbard_correction.py
-samba_ilum/src/job.py
-samba_ilum/src/kpoints.py
-samba_ilum/src/lattice_plot3d.py
-samba_ilum/src/make_files.py
-samba_ilum/src/output.py
-samba_ilum/src/poscar_fix_direct_coord.py
-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.py
-samba_ilum/src/xyz-scan_analysis.py
-samba_ilum/src/z-scan.py
-samba_ilum/src/z-scan_analysis.py
-samba_ilum/src/INPUTS/Hubbard_U_values.txt
-samba_ilum/src/INPUTS/INCAR_a-scan
-samba_ilum/src/INPUTS/INCAR_bader
-samba_ilum/src/INPUTS/INCAR_bader.SO
-samba_ilum/src/INPUTS/INCAR_bands
-samba_ilum/src/INPUTS/INCAR_bands.SO
-samba_ilum/src/INPUTS/INCAR_dos
-samba_ilum/src/INPUTS/INCAR_dos.SO
-samba_ilum/src/INPUTS/INCAR_relax
-samba_ilum/src/INPUTS/INCAR_scf
-samba_ilum/src/INPUTS/INCAR_scf.SO
-samba_ilum/src/INPUTS/INCAR_xy-scan
-samba_ilum/src/INPUTS/INCAR_xyz-scan
-samba_ilum/src/INPUTS/INCAR_z-scan
-samba_ilum/src/INPUTS/SAMBA_HeteroStructure.input
-samba_ilum/src/INPUTS/SAMBA_WorkFlow.input
-samba_ilum/src/INPUTS/vdw_kernel.bindat
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.bands
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.chgcar
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.dos
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.location
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.locpot
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.orbitals
-samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.spin

samba_ilum-1.1.0.116/SAMBA_ilum.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-samba_ilum = samba_ilum:main