vasprocar 1.1.19.165__tar.gz → 1.1.19.168__tar.gz

vasprocar-1.1.19.168/PKG-INFO

@@ -0,0 +1,17 @@
+Metadata-Version: 2.1
+Name: vasprocar
+Version: 1.1.19.168
+Summary: VASProcar is an open-source package written in the Python 3 programming language, which aims to provide an intuitive tool for the post-processing of the output files produced by the DFT VASP/QE codes, through an interactive user interface.
+Home-page: https://doi.org/10.5281/zenodo.6343960
+Download-URL: https://doi.org/10.5281/zenodo.6343960
+Author: Augusto de Lelis Araujo and Renan da Paixao Maciel
+Author-email: augusto-lelis@outlook.com, renan.maciel@physics.uu.se
+License: GNU GPLv3
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.24.1
+Requires-Dist: scipy>=1.10.0
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: plotly>=5.13.0
+Requires-Dist: moviepy>=1.0.2
+Requires-Dist: kaleido>=0.2.1
+Requires-Dist: requests>=2.31.0

vasprocar-1.1.19.168/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{vasprocar-1.1.19.165 → vasprocar-1.1.19.168}/setup.py

@@ -1,18 +1,18 @@
 from distutils.core import setup
 from setuptools import setup, find_packages
+import json
 from pathlib import Path
 from typing import Optional
-import json
 
 setup(
     name = "vasprocar",
-    version = "1.1.19.165",
-    packages=['vasprocar', 'vasprocar.src'],
-    include_package_data=True,
-    entry_points={'console_scripts': ['vasprocar = vasprocar.__main__:main']},
+    version = "1.1.19.168",
+    entry_points={'console_scripts': ['vasprocar = vasprocar:main']},
     description = "VASProcar is an open-source package written in the Python 3 programming language, which aims to provide an intuitive tool for the post-processing of the output files produced by the DFT VASP/QE codes, through an interactive user interface.",
-    author = "Augusto de Lelis Araujo and Renan da Paixao Maciel",
+    author = "Augusto de Lelis Araujo and Renan da Paixao Maciel", 
     author_email = "augusto-lelis@outlook.com, renan.maciel@physics.uu.se",
+    url = "https://doi.org/10.5281/zenodo.6343960",
+    download_url = "https://doi.org/10.5281/zenodo.6343960",
     license = "GNU GPLv3",
     install_requires=['numpy>=1.24.1',
                       'scipy>=1.10.0',
@@ -21,9 +21,10 @@ setup(
                       'moviepy>=1.0.2',
                       'kaleido>=0.2.1',
                       'requests>=2.31.0'],
-    package_data={'samba_ilum': ['*.dat', '*.png', '*.jpg', '*']},
+    package_data={"": ['*.dat', '*.png', '*.jpg', '*']},
 )
 
+
 # python3 -m pip install --upgrade twine
 # python setup.py sdist
 # python -m twine upload dist/*

vasprocar-1.1.19.168/vasprocar/__main__.py

@@ -0,0 +1,153 @@
+# VASProcar Copyright (C) 2023
+# GNU GPL-3.0 license
+
+import os
+import sys
+import shutil
+import requests
+
+#----------------
+main_dir = 'src/'
+dir_files = os.getcwd()
+os.chdir(os.path.dirname(os.path.realpath(__file__)))
+dir_vasprocar = os.path.dirname(os.path.realpath(__file__))
+print(f'{dir_vasprocar}')
+#------------------------
+
+version = '1.1.19.168'
+VASProcar_name = 'VASProcar version ' + version
+
+url_1 = 'https://pypi.org/project/vasprocar'
+url_2 = 'https://doi.org/10.5281/zenodo.6343960'
+url_3 = 'https://github.com/Augusto-de-Lelis-Araujo/VASProcar-Python-tools-VASP'
+
+print(" ")
+print("######################################################################")
+print(f'# {VASProcar_name} Copyright (C) 2023')
+print(f'# GNU GPL-3.0 license')
+print("# ====================================================================")
+print(f'# {url_1} ')
+print(f'# {url_2} ')
+print(f'# {url_3} ')
+print("######################################################################")
+print("# Authors:                                                            ")
+print("# ====================================================================")
+print("# Augusto de Lelis Araujo                                             ")
+print("# [2022-2024] CNPEM|Ilum|LNNano (Campinas-SP/Brazil),                 ")
+print("# [2007-2022] Federal University of Uberlandia (Uberlândia-MG/Brazil) ")
+print("# e-mail: augusto-lelis@outlook.com                                   ")
+print("# ====================================================================")
+print("# Renan da Paixao Maciel                                              ")
+print("# [2020-2024] Uppsala University (Uppsala/Sweden),                    ")
+print("# [2014-2020] Federal University of Uberlandia (Uberlândia-MG/Brazil) ")
+# print("# e-mail: renan.maciel@physics.uu.se                                  ")
+print("######################################################################")
+
+print("                                                         ")
+print(" _    _____   _____ ____  ____  ____  _________    ____  ")
+print("| |  / /   | / ___// __ \/ __ \/ __ \/ ____/   |  / __ \ ")
+print("| | / / /| | \__ \/ /_/ / /_/ / / / / /   / /| | / /_/ / ")
+print("| |/ / ___ |___/ / ____/ _, _/ /_/ / /___/ ___ |/ _, _/  ")
+print("|___/_/  |_/____/_/   /_/ |_|\____/\____/_/  |_/_/ |_|   ")
+print(f'                                                      v{version}')
+print("                                                         ")
+
+#------------------------------------------------------------------------------
+# Adding the contribution of all orbitals to the Spin components (Sx|Sy|Sz) ---
+#------------------------------------------------------------------------------
+Orb_spin = [1]*16
+
+#----------------------------------------------------
+# code execution ------------------------------------
+#----------------------------------------------------
+
+run = main_dir + '_dft.py'
+exec(open(run).read())
+
+run = main_dir + 'inputs/' + 'inputs.py'
+exec(open(run).read())
+
+if (len(inputs) == 0 and DFT == '_?/'):
+
+   print("######################################################################")
+   print("# Which package was used for the DFT calculations? ===================")
+   print("# [1] VASP (Vienna Ab initio Simulation Package)                      ")
+   print("# [2] QE   (Quantum ESPRESSO)                                         ")
+   print("######################################################################")   
+   pacote_dft = input(" "); pacote_dft = int(pacote_dft)
+   print(" ")
+
+   if (pacote_dft == 1): DFT = '_VASP/' 
+   if (pacote_dft == 2): DFT = '_QE/'
+
+if (DFT == '_VASP/'):
+   print("######################################################################")
+   print("## VASP (Vienna Ab initio Simulation Package) ===================== ##")
+   print("## Tested versions: 5.4.4, 6.2, 6.4.3 ============================= ##")
+   print("## ================================================================ ##")
+   print("# Basic files to execute the code: CONTCAR, KPOINTS, OUTCAR, PROCAR ##")
+   print("# For other features: DOSCAR, LOCPOT, WAVECAR or vasprun.xml        ##")
+   print("######################################################################")   
+   print(" ")
+
+if (DFT == '_QE/'):
+   print("######################################################################")
+   print("## QE (Quantum ESPRESSO) >> Tested versions: 6.4.1 and 7.1 ======== ##")
+   print("## ================================================================ ##")
+   print("# Basic files to execute the code: scf.in, scf.out, nscf.in,        ##")
+   print("#                                  nscf.out, bands.in, bands.out    ##")
+   print("# For other features: projwfc.in, projwfc.out, 'filband',           ##")
+   print("#                     'filproj'.projwfc_up and 'filpdos'.pdos_atm   ##")
+   print("######################################################################")   
+   print(" ")
+   #---------------------
+   read_contribuicao = 0
+   read_projwfc_up = 0
+   read_proj_J = 0
+
+#------------------------------------------------
+# Checking for updates for VASProcar ------------
+#------------------------------------------------
+try:
+    url = f"https://pypi.org/pypi/{'vasprocar'}/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 VASProcar version is out of date !!!        ")
+       print("--------------------------------------------------------------")
+       print("To update, close the VASProcar and enter into the terminal:   ")
+       print("              pip install --upgrade vasprocar                 ")
+       print("--------------------------------------------------------------")
+       print(" ")
+       print(" ")
+    ...
+except Exception as e:
+    print("--------------------------------------------------------------")
+    print("   !!! Unable to verify the current version of VASProcar !!!  ")
+    print("--------------------------------------------------------------") 
+    print(" ")
+
+if (len(inputs) == 0):
+   run = main_dir + '_settings.py'
+   exec(open(run).read())
+
+if (len(inputs) > 0):
+   for inp in range(len(inputs)): 
+       #---------------------------------------------------------------------------
+       exec(open(dir_files + '/inputs/' + 'input.vasprocar.' + inputs[inp]).read())
+       #---------------------------------------------------------------------------
+       if (inputs[inp] == 'bands'):         opcao = -10
+       if (inputs[inp] == 'spin'):          opcao = -20
+       if (inputs[inp] == 'orbitals'):      opcao = -30
+       if (inputs[inp] == 'dos'):           opcao = -31
+       if (inputs[inp] == 'location'):      opcao = -32
+       if (inputs[inp] == 'locpot'):        opcao = -40
+       if (inputs[inp] == 'chgcar'):        opcao = -41
+       if (inputs[inp] == 'spin_video'):    opcao = -23
+       if (inputs[inp] == 'fermi_surface'): opcao = -11
+       #-----------------------------------------------
+       run = main_dir + '_settings.py'
+       exec(open(run).read())

{vasprocar-1.1.19.165 → vasprocar-1.1.19.168}/vasprocar/src/_VASP/_nscf.py

@@ -164,8 +164,10 @@ for wp in range(1, (n_procar+1)):
             # Calculating the PROCAR file reading percentage ----------------------
             #----------------------------------------------------------------------
 
+            """
+            #----------------------
             porc = (point_k/nk)*100        
-
+            #-----------------
             if (porc >= temp):
                # print(f'\rAnalyzed  {porc:>3,.0f}%', end='')    # informação imprimida sempre na mesma linha 
                print(f'Analyzed  {porc:>3,.0f}%')                # informação imprimida em linhas consecutivas 
@@ -176,6 +178,19 @@ for wp in range(1, (n_procar+1)):
                   temp = 25.0
                if (number >= 3):
                   temp = temp + 25.0
+            """
+
+            #----------
+            number += 1
+            porc = (point_k/nk)*100        
+            #----------------------
+            if porc >= temp:
+               bar_length = 50
+               filled_length = int(bar_length * porc // 100)
+               bar = '#' * filled_length + '-' * (bar_length - filled_length)
+               print(f'\rProgress: |{bar}| {porc:.1f}%', end="")
+               sys.stdout.flush()
+               temp += 1 # Atualiza a cada 1%
               
             #----------------------------------------------------------------------
             # Reading the k1, k2 and k3 coordinates of each k-point ---------------

{vasprocar-1.1.19.165 → vasprocar-1.1.19.168}/vasprocar/src/_VASP/contribuicao.py

@@ -210,9 +210,9 @@ if (penetration_plot == 1):
        if (dirc_p_length == 1): Coord[i] = ((C1*A1x) + (C2*A2x) + (C3*A3x))*Parametro
        if (dirc_p_length == 2): Coord[i] = ((C1*A1y) + (C2*A2y) + (C3*A3y))*Parametro
        if (dirc_p_length == 3): Coord[i] = ((C1*A1z) + (C2*A2z) + (C3*A3z))*Parametro
-#------------------------------------
-p_max = abs( max(Coord) -min(Coord) )
-#------------------------------------
+   #------------------------------------
+   p_max = abs( max(Coord) -min(Coord) )
+   #------------------------------------
 
 #######################################################################
 # Obtaining the results from DFT outpout files ########################
@@ -751,64 +751,65 @@ if (penetration_plot == 1):
    #---------------
 
 
-print(" ")
-print ("======== Plotting the penetration length (Matplotlib) ========")
+if (penetration_plot == 1):
+   print(" ")
+   print ("======== Plotting the penetration length (Matplotlib) ========")
 
-print(" ")
-print(".........................")
-print("..... Wait a moment .....")
-print(".........................")
+   print(" ")
+   print(".........................")
+   print("..... Wait a moment .....")
+   print(".........................")
 
-#======================================================================
-#======================================================================
-# File Structure for Plot via Matplotlib ==============================
-#======================================================================
-#======================================================================   
+   #======================================================================
+   #======================================================================
+   # File Structure for Plot via Matplotlib ==============================
+   #======================================================================
+   #======================================================================   
 
-p_length = np.loadtxt(dir_files + '/output/Contributions/p_length.dat') 
-p_length.shape
+   p_length = np.loadtxt(dir_files + '/output/Contributions/p_length.dat') 
+   p_length.shape
 
-x = p_length[:,0]
+   x = p_length[:,0]
 
-fig, ax = plt.subplots()
+   fig, ax = plt.subplots()
 
-# Plot of Bands =======================================================
+   # Plot of Bands =======================================================
 
-for i in range (1,((bands_f -bands_i)+1)):
-    y = p_length[:,i]
+   for i in range (1,((bands_f -bands_i)+1)):
+       y = p_length[:,i]
 
-    """
-    # Interpolando os dados ======================================
-    grau_polinomio = 12;  nd = 250
-    # Calcula os coeficientes do polinômio -----------------------
-    coeficientes = np.polyfit(x, y, grau_polinomio)
-    # Criando a função de interpolação ---------------------------
-    polinomio_interpolador = np.poly1d(coeficientes)
-    # Gerando mais pontos por interpolação -----------------------
-    x_interp = np.linspace(min(x), max(x), nd)
-    y_interp = polinomio_interpolador(x_interp)
-    #=============================================================
-    """
+       """
+       # Interpolando os dados ======================================
+       grau_polinomio = 12;  nd = 250
+       # Calcula os coeficientes do polinômio -----------------------
+       coeficientes = np.polyfit(x, y, grau_polinomio)
+       # Criando a função de interpolação ---------------------------
+       polinomio_interpolador = np.poly1d(coeficientes)
+       # Gerando mais pontos por interpolação -----------------------
+       x_interp = np.linspace(min(x), max(x), nd)
+       y_interp = polinomio_interpolador(x_interp)
+       #=============================================================
+       """
 
-    plt.plot(x, y, color = 'black', linestyle = '-', linewidth = 0.25) 
-    # plt.plot(x_interp, y_interp, color = 'black', linestyle = '-', linewidth = 0.25)
-    # plt.scatter(x, y, s = 5, color = 'black', marker='o', alpha = 1.0, edgecolors = 'none')
+       plt.plot(x, y, color = 'black', linestyle = '-', linewidth = 0.25) 
+       # plt.plot(x_interp, y_interp, color = 'black', linestyle = '-', linewidth = 0.25)
+       # plt.scatter(x, y, s = 5, color = 'black', marker='o', alpha = 1.0, edgecolors = 'none')
 
-#======================================================================
+   #======================================================================
 
-plt.xlim((x[0], x[(n_procar*nk)-1]))
-plt.ylim((0.0, p_max*(1.05)))
+   plt.xlim((x[0], x[(n_procar*nk)-1]))
+   plt.ylim((0.0, p_max*(1.05)))
 
-if (Dimensao == 1): plt.xlabel('$2{\pi}/{a}$')
-if (Dimensao == 2): plt.xlabel('${\AA}^{-1}$')
-if (Dimensao == 3): plt.xlabel('${nm}^{-1}$')
-#--------------------------------------------
-plt.ylabel('penetration length (${\AA}$)')
+   if (Dimensao == 1): plt.xlabel('$2{\pi}/{a}$')
+   if (Dimensao == 2): plt.xlabel('${\AA}^{-1}$')
+   if (Dimensao == 3): plt.xlabel('${nm}^{-1}$')
+   #--------------------------------------------
+   plt.ylabel('penetration length (${\AA}$)')
 
-ax.set_box_aspect(1.25/1.0)
+   ax.set_box_aspect(1.25/1.0)
     
-plt.savefig(dir_files + '/output/Contributions/penetration_length.png', dpi = 600, bbox_inches='tight', pad_inches=0)
-# plt.show()
+   plt.savefig(dir_files + '/output/Contributions/penetration_length.png', dpi = 600, bbox_inches='tight', pad_inches=0)
+   # plt.show()
 
 
 #---------

{vasprocar-1.1.19.165 → vasprocar-1.1.19.168}/vasprocar/src/_settings.py

@@ -170,9 +170,8 @@ if (len(inputs) == 0 and DFT == '_VASP/'):
 
    if (opcao == 5 or opcao == -5):
       print("## ======================================================== ##")
-      # print("## [50] POSCAR: Convert ion coord. (Cartesian <> Direct)    ##")
-      print("## [51] POSCAR: Ion substitution in the lattice             ##")
-      print("## [52] Generate KPOINTS file (2D Plane or 3D Mesh in ZB)   ##")
+      print("## [51] Generate KPOINTS file (2D Plane or 3D Mesh in ZB)   ##")
+      print("## [52] POSCAR - Ion substitution in the lattice            ##")
       print("## [53] Combining/Merging different POTCAR files            ##")
       print("## [54] Tip: Using Multiple PROCAR Files                    ##")
       print("## [55] Check and fix VASP output files                     ##")
@@ -241,7 +240,7 @@ shutil.copyfile(source, destination)
 # Getting information from CONTCAR/OUTCAR/PROCAR files: ----------------
 # ----------------------------------------------------------------------
 
-if (opcao > -100 and opcao < 100 and opcao != 41 and opcao != -41 and opcao != 50 and opcao != 51 and opcao != -51 and opcao != 52 and opcao != -52 and opcao != 53 and opcao != -53 and opcao != 6 and opcao != -6):
+if (opcao > -100 and opcao < 100 and opcao != 41 and opcao != -41 and opcao != 51 and opcao != -51 and opcao != 52 and opcao != -52 and opcao != 53 and opcao != -53 and opcao != 6 and opcao != -6):
    execute_python_file(filename = DFT + '_info_b.py')
 
    print("#######################################################################")
@@ -366,12 +365,12 @@ if (opcao == 43 or opcao == -43):
 # if (opcao == 44 or opcao == -44):
 #    execute_python_file(filename = DFT + 'wave_function.py')
 
-if (opcao == 52 or opcao == -50):
-   execute_python_file(filename = DFT + 'poscar_converter_coord.py')
-
-if (opcao == 51 or opcao == -52):
+if (opcao == 51 or opcao == -51):
    execute_python_file(filename = DFT + 'kpoints_2D_3D.py')
 
+if (opcao == 52 or opcao == -52):
+   execute_python_file(filename = DFT + 'poscar_replace.py')
+
 if (opcao == 53 or opcao == -53):
    execute_python_file(filename = DFT + 'postar_combination.py')
 

{vasprocar-1.1.19.165 → vasprocar-1.1.19.168}/vasprocar/src/etc/BibTeX.dat

@@ -3,7 +3,7 @@
   title        = {VASProcar: Python tools for DFT calculations},
   year         = 2024,
   publisher    = {Zenodo},
-  version      = {1.1.19.100},
+  version      = {1.1.19.167},
   doi          = {10.5281/zenodo.6343960},
   url          = {https://doi.org/10.5281/zenodo.6343960}
 }

vasprocar-1.1.19.168/vasprocar/src/etc/codes_append/CONTCAR.vasp

@@ -0,0 +1,164 @@
+SAMBA Cr_S_Br_Cr_S_Br+B_N_C 60 96 | mism
+   1.00000000000000
+   -14.2848791339220007   -3.9742969419600001    0.0000000000000000
+     9.4427924565130006   -3.2698878045819999    0.0000000000000000
+     0.0000000000000000    0.0000000000000000   36.7872736853993203
+   Cr   S    Br   Cr   S    Br   B    N    C
+    10    10    10    10    10    10    16    16    64
+Direct
+  0.7216418491804446  0.7802683482026536  0.2516312833563739
+  0.8780309470996506  0.5454705386439342  0.2511596859072942
+  0.1111380607560886  0.4413657730432700  0.2513060512004112
+  0.2765097309695088  0.2174534553398188  0.2517542343481489
+  0.5105635207818731  0.0177519789218137  0.2525668139196751
+  0.2253184987993928  0.7866933980797632  0.2879959901801953
+  0.3907856066959419  0.5616426437040741  0.2878519793933106
+  0.6179996895812080  0.4466305434829267  0.2875036486401972
+  0.7789952219626167  0.2195374164256177  0.2879620662815833
+ -0.0044538782946559 -0.0064578187980475  0.2875020405916372
+  0.0951535901644982  0.8972029098112618  0.2882517248411755
+  0.3128666673711351  0.6941493382816437  0.2936876842174231
+  0.4985661142645004  0.4974040864765907  0.2870271532003814
+  0.6892611461684213  0.3074430377809068  0.2965197950688825
+  0.9045900820889426  0.1024314857997449  0.2882109282086890
+  0.5986753383078536  0.9037518612174892  0.2510931235693188
+  0.8115194383773044  0.6924898577166017  0.2433884997236462
+  0.0026828488200672  0.5061183651633484  0.2539463140472442
+  0.1907241763429654  0.3119930445401586  0.2453260325189788
+  0.4035232082846536  0.1012320374846992  0.2510439349314766
+  0.1026994711430902  0.9049883751625564  0.2040932664389696
+  0.3039545381493547  0.7203274849387065  0.2008364608629013
+  0.4995099832483352  0.5007117490930835  0.2047376189209838
+  0.6973925480312552  0.2808085654332395  0.2002427508940794
+  0.8969195994105555  0.0957974755125581  0.2037420428060845
+  0.6049422068244550  0.9086737679887940  0.3361771624578482
+  0.8056185366055998  0.7175815765423890  0.3385161797860979
+  0.0012603620743749  0.5005167719723704  0.3357567474228698
+  0.1965812799052423  0.2864453431523405  0.3381585373473621
+  0.3965065732195256  0.0929063396202327  0.3366371894870163
+  0.7402093103203246  0.8246406682319410  0.4404442078548286
+  0.9302128414416627  0.6361301859765187  0.4415608909180711
+  0.0862331559107781  0.3493852526274828  0.4415587811046937
+  0.2738060214345500  0.1468333839622619  0.4423153110409600
+  0.5161445321416231 -0.0143991439957963  0.4433083352650889
+  0.1950872598867735  0.8020974223614233  0.4773120304823328
+  0.3872616559428482  0.6177955073447737  0.4778963562653214
+  0.6268646192150717  0.4689094818973356  0.4768978510971592
+  0.7713410375833726  0.2012330536358750  0.4776176849002763
+ -0.0221142035750197 -0.0173649743992196  0.4781093270834843
+  0.0975599164615978  0.8939479004060608  0.4883350330439605
+  0.2983974422811094  0.7150327284620741  0.4797534016193755
+  0.5154584644916244  0.5198312257802414  0.4780177542491482
+  0.6818628657513099  0.2986274029428298  0.4820923308698185
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