SAMBA-ilum 1.0.0.417__tar.gz → 1.0.0.419__tar.gz

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.417
+Version: 1.0.0.419
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/SAMBA_ilum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SAMBA_ilum
-Version: 1.0.0.417
+Version: 1.0.0.419
 Summary: ...
 Author: Augusto de Lelis Araujo
 Author-email: augusto-lelis@outlook.com

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/__main__.py

@@ -16,7 +16,7 @@ dir_samba = os.path.dirname(os.path.realpath(__file__))
 print(f'{dir_samba}')
 #--------------------
 
-version = '1.0.0.417'
+version = '1.0.0.419'
 
 print(" ")
 print("=============================================================")

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/BZ_2D.py

@@ -1,5 +1,6 @@
 #-----------------
 import numpy as np
+import sys
 import os
 #----------------
 import matplotlib
@@ -16,9 +17,15 @@ from scipy.spatial import Voronoi
 #============================================================
 kpoints_file = []
 kpath = []
-#---------
-if os.path.isdir('output/Bandas'):     dir_kpath = 'bands'
-if os.path.isdir('output/Bandas.SO'):  dir_kpath = 'bands.SO'
+#-------------------
+continue_plot_bz = 0
+if os.path.isdir('output/Bandas'):
+   dir_kpath = 'bands'
+   continue_plot_bz = 1
+if os.path.isdir('output/Bandas_SO'):
+   dir_kpath = 'bands.SO'
+   continue_plot_bz = 1
+if (continue_plot_bz == 0): sys.exit()
 #-----------------------------------------------------------------------------
 if os.path.isfile(dir_kpath + '/' + 'KPOINTS'): kpoints_file.append('KPOINTS')
 #--------------------------------------------------------------------------------------
@@ -159,5 +166,5 @@ ax.legend(loc = "lower left", title = "", fontsize=8)
 ax.set_box_aspect(abs((y_max - y_min) / (x_max - x_min)))
 #-------------------------------------------------------------------------------------------------------------------------------
 if os.path.isdir('output/Bandas'): plt.savefig('output/Bandas/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
-if os.path.isdir('output/Bandas.SO'): plt.savefig('output/Bandas.SO/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
+if os.path.isdir('output/Bandas_SO'): plt.savefig('output/Bandas_SO/Brillouin_Zone.png', dpi = 600, bbox_inches='tight', pad_inches=0)
 #-------------------------------------------------------------------------------------------------------------------------------------

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/INPUTS/INCAR_xy-scan

@@ -1,6 +1,6 @@
 SYSTEM = "VASP"
 NELMIN = 4
-NELM = 60
+NELM = 120
 EDIFF = 1E-6
 EDIFFG = -1E-3
 # replace_ispin

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/INPUTS/INCAR_xyz-scan

@@ -1,6 +1,6 @@
 SYSTEM = "VASP"
 NELMIN = 4
-NELM = 60
+NELM = 120
 EDIFF = 1E-6
 EDIFFG = -1E-3
 # replace_ispin

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/INPUTS/INCAR_z-scan

@@ -1,6 +1,6 @@
 SYSTEM = "VASP"
 NELMIN = 4
-NELM = 60
+NELM = 120
 EDIFF = 1E-6
 EDIFFG = -1E-3
 # replace_ispin

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/job.py

@@ -45,6 +45,10 @@ job = open(dir_out + '/job0.sh', "w")
 #====================================
 job.write(f'#!/bin/bash \n')
 job.write(f' \n')
+job.write(f'cd $dir0 \n'
+job.write(f'mv python_virtual python_virtual_delete \n'
+job.write(f'rm -r python_virtual_delete \n'
+job.write(f' \n')
 job.write(f'#------------------------------- \n')
 job.write(f'dir_virtual="{dir_virtual_python}" \n')
 job.write(f'# cp -r $dir_virtual $dir0/python_virtual \n')
@@ -391,6 +395,7 @@ job.write(f'               fi \n')
 job.write(f'           done \n')
 job.write(f'           cd $dir0/$i \n')
 job.write(f'           python3 output.py \n')
+job.write(f'           python3 BZ_2D.py \n')
 job.write(f'           python3 lattice_plot3d.py \n')
 job.write(f'           #------------------------ \n')
 job.write(f'           cp -r $dir0/$i/output/POSCAR $dir0/$i/output/POSCAR.info  \n')

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/make_files.py

@@ -639,10 +639,11 @@ for i in range(len(files)):
 # Copiando códigos python para o diretorio principal -----------------------------
 #---------------------------------------------------------------------------------
 for i in range(len(files)):
+    shutil.copyfile(dir_codes + '/data-base_json.py', dir_out + '/' + files[i] + '/data-base_json.py')
     shutil.copyfile(dir_codes + '/lattice_plot3d.py', dir_out + '/' + files[i] + '/lattice_plot3d.py')
     shutil.copyfile(dir_codes + '/output.py', dir_out + '/' + files[i] + '/output.py')
-    #-------------------------------------------------------------------------------------------------
-    shutil.copyfile(dir_codes + '/data-base_json.py', dir_out + '/' + files[i] + '/data-base_json.py')
+    shutil.copyfile(dir_codes + '/BZ_2D.py', dir_out + '/' + files[i] + '/BZ_2D.py')
+    #-------------------------------------------------------------------------------
     dir_file = dir_out + '/' + files[i] + '/data-base_json.py'
     with open(dir_file, "r") as file:  content = file.read()
     content = content.replace('# replace_type_pseudo', 'pseudo_type = ' + "'" + str(replace_type_pseudo) + "'")

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/xy-scan.py

@@ -78,8 +78,8 @@ for i in range(len(folders)):  shutil.rmtree('folders[i]')
 poscar = open('POSCAR', "r")
 #---------------------------------
 line_0 = poscar.readline().split()
-if (line_0[-5] == 'Shift_plane'):  shift = str(line_0[-5])
-if (line_0[-5] != 'Shift_plane'):  shift = '0.0_0.0'
+if (line_0[-7] == 'Shift_plane'):  shift = str(line_0[-5])
+if (line_0[-7] != 'Shift_plane'):  shift = '0.0_0.0'
 #-----------------------------------------------
 VTemp = poscar.readline();  param = float(VTemp)
 VTemp = poscar.readline().split();  A1x = float(VTemp[0]);  A1y = float(VTemp[1]);  A1z = float(VTemp[2])

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/samba_ilum/src/xy-scan_analysis.py

@@ -23,6 +23,7 @@ from matplotlib import pyplot as plt
 import matplotlib.ticker as ticker
 from mpl_toolkits.mplot3d.axes3d import Axes3D
 from matplotlib.ticker import LinearLocator, FormatStrFormatter
+import matplotlib.patheffects as path_effects
 import matplotlib.colors as mcolors
 #----------------------------------
 
@@ -69,14 +70,10 @@ delta    = date_shift[line]
 delta_min = delta.replace('_', ' ').split()
 a1_min = float(delta_min[0])
 a2_min = float(delta_min[1])
-x_min = (a1_min*A1x) + (a2_min*A2x)
-y_min = (a1_min*A1y) + (a2_min*A2y)
-#----------------------------------
+#--------------------------------
 if (a1_min == -0.0): a1_min = 0.0
 if (a2_min == -0.0): a2_min = 0.0
-if (x_min == -0.0):  x_min = 0.0
-if (y_min == -0.0):  y_min = 0.0
-#-------------------------------
+#--------------------------------
 
 
 #===============================================
@@ -102,7 +99,7 @@ for i in range(len(date_shift)):
             t_shift_A1 = shift_A1 -a1_min +shift[j]
             t_shift_A2 = shift_A2 -a2_min +shift[k]
             if (t_shift_A1 >= -0.2  and t_shift_A1 <= 1.2):
-               if (t_shift_A2 >= -0.2  and t_shift_A2 <= 1.2): 
+               if (t_shift_A2 >= -0.2  and t_shift_A2 <= 1.2):
                   file.write(f'{t_shift_A1}_{t_shift_A2} {(date_E[i]*1000)/Area} \n')
 #-----------
 file.close()
@@ -126,7 +123,7 @@ file = open('xy-scan_direct.dat', "w")
 for i in range(len(date_shift)):
     VTemp = str(date_shift[i])
     VTemp = VTemp.replace('_', ' ')
-    file.write(f'{VTemp} {(date_E[i]*1000)/Area} \n')
+    file.write(f'{VTemp} {date_E[i]} \n')
 #-----------
 file.close()
 #-----------
@@ -140,7 +137,7 @@ for i in range(len(date_shift)):
     VTemp = VTemp.replace('_', ' ').split()
     Coord_X = ((float(VTemp[0])*A1x) + (float(VTemp[1])*A2x))
     Coord_Y = ((float(VTemp[0])*A1y) + (float(VTemp[1])*A2y))
-    file.write(f'{Coord_X} {Coord_Y} {(date_E[i]*1000)/Area} \n')
+    file.write(f'{Coord_X} {Coord_Y} {date_E[i]} \n')
 #-----------
 file.close()
 #-----------
@@ -225,14 +222,14 @@ cmap_gray = (mpl.colors.ListedColormap(['darkgray', 'darkgray']))
 #-----------------------
 fig, ax = plt.subplots()
 cp = plt.contourf(x_grid, y_grid, (e2_grid -E_min), levels = n_contour, cmap = 'jet', alpha = 1.0, antialiased = True)
-plt.quiver(0, 0, A1x, A1y, angles='xy', scale_units='xy', scale=1, color='black', label='A$_1$')
-plt.quiver(0, 0, A2x, A2y, angles='xy', scale_units='xy', scale=1, color='black', label='A$_2$')
+plt.quiver(0, 0, A1x, A1y, angles='xy', scale_units='xy', scale=1, color='red', label='A$_1$', linewidth=0.1, edgecolor='black')
+plt.quiver(0, 0, A2x, A2y, angles='xy', scale_units='xy', scale=1, color='red', label='A$_2$', linewidth=0.1, edgecolor='black')
 plt.plot([A1x, (A1x+A2x)], [A1y, (A1y+A2y)], color = 'black', linewidth = 1.0, zorder=3)
 plt.plot([A2x, (A1x+A2x)], [A2y, (A1y+A2y)], color = 'black', linewidth = 1.0, zorder=3)
-plt.text((A1x/2), (A1y/2), "A$_1$", fontsize=10, color="black")
-plt.text((A2x/2), (A2y/2), "A$_2$", fontsize=10, color="black")
-# plt.scatter(delta_X, delta_Y, c='black', marker='o', s=2)
-# plt.scatter(x_min, y_min, c='black', marker='o', s=2)
+text1 = plt.text((A1x/2), (A1y/2), "A$_1$", fontsize=10, color="red")
+text2 = plt.text((A2x/2), (A2y/2), "A$_2$", fontsize=10, color="red")
+text1.set_path_effects([path_effects.Stroke(linewidth=0.2, foreground='black'), path_effects.Normal()])
+text2.set_path_effects([path_effects.Stroke(linewidth=0.2, foreground='black'), path_effects.Normal()])
 cbar = fig.colorbar(cp, orientation = 'vertical', shrink = 1.0)
 #-------------------
 plt.title('xy-scan')
@@ -255,16 +252,31 @@ shutil.copyfile(str(delta) + '/CONTCAR', 'CONTCAR')
 #--------------------------------------------------
 
 
+#-----------------------------
+contcar = open('CONTCAR', "r")
+#----------------------------------
+line_0 = contcar.readline().split()
+if (line_0[-7] == 'Shift_plane'):
+   shift_0 = str(line_0[-5])
+   shift_0 = shift_0.replace('_', ' ').split()
+   #------------------------------------------
+   shift_A1 = float(shift_0[0])
+   shift_A2 = float(shift_0[1])
+   shift_X = (shift_A1*A1x) + (shift_A2*A2x)
+   shift_Y = (shift_A1*A1y) + (shift_A2*A2y)
+   #----------------------------------------
+contcar.close()
+#--------------
+
+
 #=====================================================
 info = open('info_xy-scan.dat', "w", encoding='utf-8')
 info.write(f'====================================================== \n')
 info.write(f'Displacement carried out over the 2nd material lattice   \n')
 #------------------------------------------------------------------
-info.write(f'Displacement_XY = ({x_min}, {y_min}) in Å \n')
-info.write(f'Displacement_XY = ({a1_min}*A1, {a2_min}*A2) \n')
+info.write(f'Displacement_XY = ({shift_X}, {shift_Y}) in Å \n')
+info.write(f'Displacement_XY = ({shift_A1}*A1, {shift_A2}*A2) \n')
 #----------------------------------------------------------------
-# info.write(f'Displacement_XY = ({delta_X}, {delta_Y}) in Å \n')
-# info.write(f'Displacement_XY = ({delta_A1}*A1, {delta_A2}*A2) \n')
 info.write(f'------------------------------------------------------ \n')
 info.write(f'ΔE = {Delta_E_meV:.12f} meV/Å^2  or  {Delta_E_J:.12f} J/m^2 \n')
 info.write(f'====================================================== \n')

{samba_ilum-1.0.0.417 → samba_ilum-1.0.0.419}/setup.py

@@ -6,7 +6,7 @@ import json
 
 setup(
     name = "SAMBA_ilum",
-    version = "1.0.0.417",
+    version = "1.0.0.419",
     entry_points={'console_scripts': ['samba_ilum = samba_ilum:main']},
     description = "...",
     author = "Augusto de Lelis Araujo",