SAMBA-ilum 1.0.0.542__tar.gz → 1.0.0.544__tar.gz

{samba_ilum-1.0.0.542 → samba_ilum-1.0.0.544}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.542
+Version: 1.0.0.544
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.542 → samba_ilum-1.0.0.544}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.542
+Version: 1.0.0.544
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.542 → samba_ilum-1.0.0.544}/SAMBA_ilum.egg-info/SOURCES.txt

@@ -31,6 +31,7 @@ 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-1.0.0.542 → samba_ilum-1.0.0.544}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.542'
+version = '1.0.0.544'
 
 print(" ")
 print("=============================================================")
@@ -125,12 +125,17 @@ if (tarefa == 1):
    separacao2 = separation_2
 
 
-   #======================================================
-   # Checking the structure of POSCAR files, regarding the 
-   # rotation angle in relation to the z-axis ============
-   #======================================================
+   #=============================================================
+   # 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):
@@ -283,8 +288,15 @@ if (tarefa == 2):
            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')

{samba_ilum-1.0.0.542 → samba_ilum-1.0.0.544}/samba_ilum/src/cell_check.py

@@ -177,7 +177,7 @@ for name in files0:
         menor_0 = min(angulos_z) if angulos_z else 0.0
         menor_1 = min(angulos_z_na_origem) if angulos_z_na_origem else 0.0
         #--------------------------------------------------------------------
-        # If there is a difference, calculate, correct and save the new file.
+        # If there is a difference, the rotation angle position is fixed ----
         #--------------------------------------------------------------------
         if (menor_0 != menor_1 and menor_0 != 0.0):
             axis_correction += 1

samba_ilum-1.0.0.544/samba_ilum/src/poscar_fix_direct_coord.py

@@ -0,0 +1,117 @@
+# SAMBA_ilum Copyright (C) 2025 - Closed source
+
+
+import numpy as np
+import shutil
+import glob
+import sys
+import os
+
+
+#------------------------------------------------------
+# Function to delete hidden files ---------------------
+#------------------------------------------------------
+def delete_hidden_files(target_directory):
+    search_files = os.path.join(target_directory, '.*')
+    for item in glob.glob(search_files):
+        try:
+            if os.path.isfile(item): os.remove(item)
+        except OSError: pass
+
+
+#------------------------------------------------------
+# Listing files inside the "dir_files_in" directory ---
+#------------------------------------------------------
+poscar_dir_path = os.path.join(dir_files, dir_files_in)
+#-----------------------------------
+delete_hidden_files(poscar_dir_path)
+files0 = [name for name in os.listdir(poscar_dir_path) if os.path.isfile(os.path.join(poscar_dir_path, name))]
+
+
+#======================================================
+# Checking/Correcting POSCAR files ====================
+#======================================================
+poscar_backup_dir_path = os.path.join(dir_files, 'POSCAR_Backup_temp')
+os.rename(poscar_dir_path, poscar_backup_dir_path)
+os.makedirs(poscar_dir_path, exist_ok=True)
+#------------------------------------------
+files1 = [name for name in os.listdir(poscar_backup_dir_path) if os.path.isfile(os.path.join(poscar_backup_dir_path, name))]
+for file_in in files1:
+    #-------------------
+    type_poscar = 'none'
+    poscar_in  = open(poscar_backup_dir_path + '/' + file_in, "r")
+    for i in range(8): VTemp = poscar_in.readline().split()
+    if (VTemp[0][0] == 'D' or VTemp[0][0] == 'd'): type_poscar = 'direct'
+    if (VTemp[0][0] == 'C' or VTemp[0][0] == 'c'): type_poscar = 'cartesian'
+    if (VTemp[0][0] == 'S' or VTemp[0][0] == 's'): type_poscar = 'selective'
+    poscar_in.close()
+    #----------------
+
+    if (type_poscar != 'cartesian'): shutil.copy2(poscar_backup_dir_path + '/' + file_in, poscar_dir_path + '/' + file_in)
+
+    if (type_poscar == 'cartesian'):
+       #-------------------------------------------------------------
+       poscar_in  = open(poscar_backup_dir_path + '/' + file_in, "r")
+       poscar_out = open(poscar_dir_path + '/' + file_in, "w")
+       #------------------------------------------------------
+       VTemp = poscar_in.readline()
+       poscar_out.write(f'{VTemp}')
+       #------------------------------------------------------------
+       VTemp = poscar_in.readline().split(); param = float(VTemp[0])
+       poscar_out.write(f'1.0 \n')
+       #-----------------------------------
+       VTemp = poscar_in.readline().split()
+       A1x = float(VTemp[0])*param
+       A1y = float(VTemp[1])*param
+       A1z = float(VTemp[2])*param
+       poscar_out.write(f'{A1x:.16} {A1y:.16} {A1z:.16} \n')
+       #----------------------------------------------------
+       VTemp = poscar_in.readline().split()
+       A2x = float(VTemp[0])*param
+       A2y = float(VTemp[1])*param
+       A2z = float(VTemp[2])*param
+       poscar_out.write(f'{A2x:.16} {A2y:.16} {A2z:.16} \n')
+       #----------------------------------------------------
+       VTemp = poscar_in.readline().split()
+       A3x = float(VTemp[0])*param
+       A3y = float(VTemp[1])*param
+       A3z = float(VTemp[2])*param
+       poscar_out.write(f'{A3x:.16} {A3y:.16} {A3z:.16} \n')
+       #----------------------------------------------------
+       VTemp = poscar_in.readline()
+       poscar_out.write(f'{VTemp}')
+       #---------------------------
+       nions = 0
+       VTemp = poscar_in.readline()
+       poscar_out.write(f'{VTemp}')
+       VTemp = VTemp.split()
+       for i in range(len(VTemp)): nions += int(VTemp[i])
+       #-------------------------------------------------
+       VTemp = poscar_in.readline()
+       poscar_out.write(f'Direct \n')
+       #-----------------------------
+       a = np.array([A1x, A1y, A1z])
+       b = np.array([A2x, A2y, A2z])
+       c = np.array([A3x, A3y, A3z])
+       T = np.linalg.inv(np.array([a, b, c]).T)      # Defines the transformation matrix
+       #---------------------------------------
+       for i in range(nions):
+           #-----------------------------------
+           VTemp = poscar_in.readline().split()
+           x = float(VTemp[0])*param
+           y = float(VTemp[1])*param
+           z = float(VTemp[2])*param
+           #------------------------
+           r = np.array([x, y, z])      # Defines the Cartesian position of the atom
+           f = np.dot(T, r)             # Calculates fractional position
+           f = f % 1.0
+           #-------------------------------------------------------
+           poscar_out.write(f'{f[0]:.16} {f[1]:.16} {f[2]:.16} \n')
+       #-----------------------------------------------------------
+       poscar_in.close()   
+       poscar_out.close()
+       #-----------------
+
+#===============================
+os.rmdir(poscar_backup_dir_path)
+#===============================

{samba_ilum-1.0.0.542 → samba_ilum-1.0.0.544}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.542",
+    version = "1.0.0.544",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",