SAMBA-ilum 1.0.0.484__tar.gz → 1.0.0.486__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/PKG-INFO +1 -1
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/SAMBA_ilum.egg-info/PKG-INFO +1 -1
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/__main__.py +1 -1
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/HeteroStructure_Generator.py +330 -427
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/setup.py +1 -1
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/LICENSE.txt +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/README.md +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/SAMBA_ilum.egg-info/SOURCES.txt +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/SAMBA_ilum.egg-info/dependency_links.txt +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/SAMBA_ilum.egg-info/entry_points.txt +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/SAMBA_ilum.egg-info/requires.txt +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/SAMBA_ilum.egg-info/top_level.txt +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/__init__.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/BZ_2D.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/HeteroStructure_Generator_OLD_1.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/HeteroStructure_Generator_OLD_2.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_a-scan +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_bader +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_bader.SO +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_bands +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_bands.SO +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_dos +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_dos.SO +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_relax +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_scf +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_scf.SO +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_xy-scan +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_xyz-scan +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/INCAR_z-scan +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/SAMBA_HeteroStructure.input +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/SAMBA_WorkFlow.input +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.bands +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.chgcar +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.dos +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.location +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.locpot +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.orbitals +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/inputs_VASProcar/input.vasprocar.spin +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/vdw_kernel.bindat +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/_info_pseudo.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/a-scan.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/a-scan_analysis.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/bader +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/bader_poscar.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/bader_update.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/charge_transfer.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/chgsum.pl +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/contcar_update.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/data-base_json.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/data-base_union.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/energy_scan.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/hubbard_correction.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/job.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/kpoints.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/lattice_plot3d.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/make_files.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/output.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/potcar.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/rotation_axis_check.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/vdW_DF.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/xy-scan.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/xy-scan_analysis.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/xyz-scan.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/xyz-scan_analysis.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/z-scan.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/z-scan_analysis.py +0 -0
- {samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/setup.cfg +0 -0
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print("")
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# from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
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from pymatgen.io.vasp import Poscar
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from pymatgen.core import Structure
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from pymatgen.analysis.structure_matcher import StructureMatcher
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#---------------------------------------------------------------
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import numpy as np
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import filecmp
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import hashlib
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import shutil
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import math
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import uuid
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import sys
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import os
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#---------------------------------------------
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#--------------------------------------------------
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# Rotulo temporário para os ions inequivalentes da célula unitária
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#----------------------------------------------------------------------------------------------------------------------------------------------
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# Rotulo temporário para os ions inequivalentes da célula unitária ----------------------------------------------------------------------------
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#----------------------------------------------------------------------------------------------------------------------------------------------
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letters = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'X', 'Z', 'Y', 'W']
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alphabet = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'X', 'Z', 'Y', 'W']
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#------------------------------------------------------
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A1 = poscar.readline().split(); A1x = float(A1[0])*param; A1y = float(A1[1])*param; A1z = float(A1[2])*param
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A2 = poscar.readline().split(); A2x = float(A2[0])*param; A2y = float(A2[1])*param; A2z = float(A2[2])*param
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A3 = poscar.readline().split(); A3x = float(A3[0])*param; A3y = float(A3[1])*param; A3z = float(A3[2])*param
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#------------------------------------------------------------------------------------------------------------
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A1x0.append(A1x); A1y0.append(A1y); A2x0.append(A2x); A2y0.append(A2y) # Armazenando os vetores A1 e A2 de cada rede
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#------------------------------------------------------------------------------------------------------------------------
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if ((A1z != 0.0) or (A2z != 0.0) or (A3x != 0.0) or (A3y != 0.0)):
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#-------------
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#---------------------------------------------------------------------------------------------------------------------------------------
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# Obtendo o menor ângulo de rotação da(s) camada(s) superiores, a fim de ajustar o ângulo de rotação final obtido na heteroestrutura ---
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#---------------------------------------------------------------------------------------------------------------------------------------
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for k in range(n_Lattice):
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#---------------------
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estrutura = Structure.from_file(dir_files + '/' + vLattice[k])
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sga = SpacegroupAnalyzer(estrutura, symprec=1e-3)
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operacoes = sga.get_symmetry_operations()
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angulos_z = []
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#-------------------
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for op in operacoes:
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R = op.rotation_matrix
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if int(round(np.linalg.det(R))) != 1: continue
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#----------------------
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z = np.array([0, 0, 1])
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Rz = R @ z
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#--------------------------------
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if np.allclose(Rz, z, atol=1e-3):
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Rxy = R[:2, :2]
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trace = np.trace(Rxy)
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cos_theta = trace / 2
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cos_theta = np.clip(cos_theta, -1.0, 1.0)
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angle = np.arccos(cos_theta)
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angle_deg = round(np.degrees(angle), 4)
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#-------------------------------------------------------------------------------------
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if 0.1 < angle_deg < 360.0 and angle_deg not in angulos_z: angulos_z.append(angle_deg)
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#--------------------------------------------------------------------------------------------
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if (k == 1):
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if angulos_z: rot_z_2 = min(angulos_z)
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#-----------------------------------------
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if angulos_z: rot_z_3 = min(angulos_z)
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#-----------------------------------------
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#-------------------------------------------------------------------------------------------------------------------------------
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# Estimando a área de cada supercélula (referente a cada Lattice), capaz de
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# Estimando a área de cada supercélula (referente a cada Lattice), capaz de abrir o range de ions [ions_crit_i, ions_crit_f] ---
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#-------------------------------------------------------------------------------------------------------------------------------
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for k in range(n_Lattice):
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#---------------------
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#-----------
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formula = []
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id_materials = []
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temp_center_x = []*3
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temp_center_y = []*3
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#-------------------
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if (dist <= temp_d):
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temp_d = dist
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new_center_x = coord_x; new_center_y = coord_y; new_center_z = 0.0
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#-------------------------------
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temp_center_x[k] = new_center_x
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temp_center_y[k] = new_center_y
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#-------------
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poscar.close()
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#-------------
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# Definir a matriz de transformação
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T = np.linalg.inv(np.array([a, b, c]).T)
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#-------------------------------------------------------------------------
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# Obtenção das coordenadas do átomo mais próximo da nova origem ----------
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#-------------------------------------------------------------------------
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poscar1 = open(diret + 'POSCAR_Supercell_' + label + '_cartesian.vasp', "r")
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#-----------------
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for i in range(2): VTemp = poscar1.readline()
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for i in range(3):
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VTemp = poscar1.readline().split(); A = [float(VTemp[0])*param, float(VTemp[1])*param]
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VTemp = poscar1.readline().split(); B = [float(VTemp[0])*param, float(VTemp[1])*param]
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#----------------------------------------------------
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for i in range(2): VTemp = poscar1.readline().split()
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center_x = 0.5*A[0] + 0.5*B[0]
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for i in range(passo):
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coord_x = float(VTemp[0])
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#------------------------
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dist = ((coord_x -center_x)**2 + (coord_y -center_y)**2)**(0.5)
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#--------------
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poscar1.close()
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#---------------------------------------------------------------------------
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poscar1 = open(diret + 'POSCAR_Supercell_' + label + '_cartesian.vasp', "r")
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poscar2 = open(diret + 'Coord_Supercell_' + label + '.dat', "r")
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poscar_new = open(temp_dir + '/temp_' + str(j+1) + '.vasp', "w")
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@@ -1085,25 +1008,28 @@ if (n_test == 1):
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1085
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for i in range(2):
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VTemp = poscar1.readline()
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poscar_new.write(f'{VTemp}')
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-
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for i in range(3):
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-
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#---------------------------------------------
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1012
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for i in range(3):
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1013
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VTemp = poscar1.readline()
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1014
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#---------------------------------------------
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poscar_new.write(f' {x1:>28,.21f} {y1:>28,.21f} {null:>28,.21f} \n')
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poscar_new.write(f' {x2:>28,.21f} {y2:>28,.21f} {null:>28,.21f} \n')
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poscar_new.write(f' {null:>28,.21f} {null:>28,.21f} {d:>28,.21f} \n')
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-
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#---------------------------------------------
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VTemp = poscar1.readline()
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1096
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poscar_new.write(f'{VTemp}')
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1097
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poscar_new.write(f'{VTemp}') # poscar_new.write(f'{s_old}')
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1021
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#---------------------------------------------
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passo = 0
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VTemp = poscar1.readline().split()
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for i in range(len(VTemp)):
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passo += int(VTemp[i])
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+
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#--------------
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poscar1.close()
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#--------------
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#####################################################################
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poscar_new.write(f'direct \n')
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#----------------------------------------------------------------------------------------------------
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@@ -1112,8 +1038,8 @@ if (n_test == 1):
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#-------------------------------------------------------------------------------------------
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for i in range(passo):
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VTemp = poscar2.readline().split()
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x = float(VTemp[0]) +
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y = float(VTemp[1]) +
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x = float(VTemp[0]) + temp_center_x[k]
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y = float(VTemp[1]) + temp_center_y[k]
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z = float(VTemp[2])
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l = str(VTemp[4])
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@@ -1316,15 +1242,7 @@ if (n_test == 1):
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# if (len(angle1) == 5): angle1 = angle1 + '00'
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# if (len(angle1) == 6): angle1 = angle1 + '0'
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#-----------------------------------------------------------------
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1319
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angle1 = angle0
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1320
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#-----------------------------------------------------------------------
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1321
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# Reduzindo angle1 à menor rotação positiva equivalente por simetria ---
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1322
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#-----------------------------------------------------------------------
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1323
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if rot_z_2 != 0.0:
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theta_mod = angle1 % rot_z_2
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angle1 = min(theta_mod, rot_z_2 - theta_mod)
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1326
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#-----------------------------------------------------------------
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1327
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angle1 = round(angle1, 4)
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1245
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+
angle1 = angle0; angle1 = round(angle1, 4)
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1328
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#=================================================================
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1329
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if (n_Lattice == 3):
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angle_V13 = np.arctan2(np.cross(V3, V1), np.dot(V3, V1)) # ângulo em radianos
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@@ -1337,15 +1255,7 @@ if (n_test == 1):
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# if (len(angle3) == 5): angle3 = angle3 + '00'
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# if (len(angle3) == 6): angle3 = angle3 + '0'
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#-----------------------------------------------------------------
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1340
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angle3 = angle2
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1341
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#-----------------------------------------------------------------------
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1342
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# Reduzindo angle3 à menor rotação positiva equivalente por simetria ---
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1343
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-
#-----------------------------------------------------------------------
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1344
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-
if rot_z_3 != 0.0:
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1345
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theta_mod = angle3 % rot_z_3
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1346
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-
angle3 = min(theta_mod, rot_z_3 - theta_mod)
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1347
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-
#-----------------------------------------------------------------
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1348
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-
angle3 = round(angle3, 4)
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1258
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+
angle3 = angle2; angle3 = round(angle3, 4)
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#====================================================================
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for j in range(3):
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VTemp1 = poscar1.readline().split()
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@@ -1363,299 +1273,298 @@ if (n_test == 1):
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1363
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if (n_Lattice == 3): poscar3.close()
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#------------------------------------
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1365
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1366
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-
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#------------------------------------------------------------------------
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1278
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+
# Escrevendo o arquivo POSCAR das Heteroestruturas: ---------------------
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1279
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+
#------------------------------------------------------------------------
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1280
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+
poscar1 = open(diret + 'Lattice1' + '/' + dir_temp_m + '/' + '/POSCAR_' + str(i+1) + '.vasp', "r")
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1281
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+
poscar2 = open(diret + 'Lattice2' + '/' + dir_temp_m + '/' + '/POSCAR_' + str(i+1) + '.vasp', "r")
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1282
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+
if (n_Lattice == 3): poscar3 = open(diret + 'Lattice3' + '/' + dir_temp_m + '/' + '/POSCAR_' + str(i+1) + '.vasp', "r")
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1283
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+
poscar_new = open(diret2 + dir_temp_m + '/POSCAR_' + str(i+1) + '.vasp', "w")
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1284
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+
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1285
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+
#-----------------------------------------------------
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1286
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+
ID_Heteroestrutura = formula_bilayer + '_' + unique_id
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1287
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+
#-----------------------------------------------------
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1288
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+
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1289
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+
#================================================
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1290
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+
VTemp1 = poscar1.readline()
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1291
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+
VTemp2 = poscar2.readline()
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1292
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+
if (n_Lattice == 3): VTemp3 = poscar3.readline()
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1293
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+
#================================================
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1294
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+
if (mismatch_type >= 0 and mismatch_type <= 3):
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1295
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+
#--------------------------
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1381
1296
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VTemp1 = poscar1.readline()
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1382
1297
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VTemp2 = poscar2.readline()
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1383
1298
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if (n_Lattice == 3): VTemp3 = poscar3.readline()
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1384
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1385
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1386
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1422
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1423
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1424
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1425
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-
# Definindo a célula intermediária ---------------------
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1426
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-
#-------------------------------------------------------
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1427
|
-
if (mismatch_type == 0):
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1428
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-
if (n_Lattice == 2):
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1429
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-
A_int = (A1 + A2_rotated)/2
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1430
|
-
B_int = (B1 + B2_rotated)/2
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1431
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-
if (n_Lattice == 3):
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1432
|
-
A_int = (A1 + A2_rotated + A3_rotated)/3
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1433
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-
B_int = (B1 + B2_rotated + B3_rotated)/3
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1434
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-
#---------------------------------------------
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1435
|
-
if (mismatch_type == 1):
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1436
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-
A_int = A1
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1437
|
-
B_int = B1
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1438
|
-
#-----------------------
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|
1439
|
-
if (mismatch_type == 2):
|
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1440
|
-
A_int = A2_rotated
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1441
|
-
B_int = B2_rotated
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1442
|
-
#-----------------------
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1443
|
-
if (mismatch_type == 3):
|
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1444
|
-
A_int = A3_rotated
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1445
|
-
B_int = B3_rotated
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1446
|
-
#--------------------------------
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|
1447
|
-
mod_A_int = np.linalg.norm(A_int)
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|
1448
|
-
mod_B_int = np.linalg.norm(B_int)
|
|
1449
|
-
Area_int = np.linalg.norm(np.cross(A_int, B_int))
|
|
1450
|
-
angle_int = np.arctan2(np.cross(A_int,B_int), np.dot(A_int,B_int))
|
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1451
|
-
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|
1452
|
-
#------------------------------------------------------------------------------------------------------------------------
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|
1453
|
-
# Utilização de vetores temporários (A,B) a fim de estimar a deformação sofrida pelas células originais -----------------
|
|
1454
|
-
#------------------------------------------------------------------------------------------------------------------------
|
|
1455
|
-
var_A1 = ((mod_A_int -mod_A1)/mod_A1)*100; var_A1 = round(var_A1, 4)
|
|
1456
|
-
var_B1 = ((mod_B_int -mod_B1)/mod_B1)*100; var_B1 = round(var_B1, 4)
|
|
1457
|
-
var_A2 = ((mod_A_int -mod_A2)/mod_A2)*100; var_A2 = round(var_A2, 4)
|
|
1458
|
-
var_B2 = ((mod_B_int -mod_B2)/mod_B2)*100; var_B2 = round(var_B2, 4)
|
|
1459
|
-
if (n_Lattice == 3):
|
|
1460
|
-
var_A3 = ((mod_A_int -mod_A3)/mod_A3)*100; var_A3 = round(var_A3, 4)
|
|
1461
|
-
var_B3 = ((mod_B_int -mod_B3)/mod_B3)*100; var_B3 = round(var_B3, 4)
|
|
1462
|
-
#--------------------------------------------------------------------------------
|
|
1463
|
-
mm_angle12 = ((angle_2 -angle_1)/angle_1)*100; mm_angle12 = round(mm_angle12, 4)
|
|
1464
|
-
mm_angle21 = ((angle_1 -angle_2)/angle_2)*100; mm_angle21 = round(mm_angle21, 4)
|
|
1465
|
-
if (n_Lattice == 3):
|
|
1466
|
-
mm_angle13 = ((angle_3 -angle_1)/angle_1)*100; mm_angle13 = round(mm_angle13, 4)
|
|
1467
|
-
mm_angle31 = ((angle_1 -angle_3)/angle_3)*100; mm_angle31 = round(mm_angle31, 4)
|
|
1468
|
-
#-----------------------------------------------------------------------------------
|
|
1469
|
-
var_angle1 = ((angle_int -angle_1)/angle_1)*100; var_angle1 = round(var_angle1, 4)
|
|
1470
|
-
var_angle2 = ((angle_int -angle_2)/angle_2)*100; var_angle2 = round(var_angle2, 4)
|
|
1471
|
-
if (n_Lattice == 3):
|
|
1472
|
-
var_angle3 = ((angle_int -angle_3)/angle_3)*100; var_angle3 = round(var_angle3, 4)
|
|
1473
|
-
#-------------------------------------------------------------------------------------
|
|
1474
|
-
mm_Area12 = ((Area2 -Area1)/Area1)*100; mm_Area12 = round(mm_Area12, 4)
|
|
1475
|
-
mm_Area21 = ((Area1 -Area2)/Area2)*100; mm_Area21 = round(mm_Area21, 4)
|
|
1476
|
-
if (n_Lattice == 3):
|
|
1477
|
-
mm_Area13 = ((Area3 -Area1)/Area1)*100; mm_Area13 = round(mm_Area13, 4)
|
|
1478
|
-
mm_Area31 = ((Area1 -Area3)/Area3)*100; mm_Area31 = round(mm_Area31, 4)
|
|
1479
|
-
#--------------------------------------------------------------------------
|
|
1480
|
-
var_Area1 = ((Area_int -Area1)/Area1)*100; var_Area1 = round(var_Area1, 4)
|
|
1481
|
-
var_Area2 = ((Area_int -Area2)/Area2)*100; var_Area2 = round(var_Area2, 4)
|
|
1482
|
-
if (n_Lattice == 3):
|
|
1483
|
-
var_Area3 = ((Area_int -Area3)/Area3)*100; var_Area3 = round(var_Area3, 4)
|
|
1484
|
-
#-----------------------------------------------------------------------------
|
|
1485
|
-
if(var_A1 == -0.0): var_A1 = 0.0
|
|
1486
|
-
if(var_B1 == -0.0): var_B1 = 0.0
|
|
1487
|
-
if(var_A2 == -0.0): var_A2 = 0.0
|
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1488
|
-
if(var_B2 == -0.0): var_B2 = 0.0
|
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1489
|
-
if(var_Area1 == -0.0): var_Area1 = 0.0
|
|
1490
|
-
if(var_Area2 == -0.0): var_Area2 = 0.0
|
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1491
|
-
if(mm_Area12 == -0.0): mm_Area12 = 0.0
|
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1492
|
-
if(mm_Area21 == -0.0): mm_Area21 = 0.0
|
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1493
|
-
if(var_angle1 == -0.0): var_angle1 = 0.0
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1494
|
-
if(var_angle2 == -0.0): var_angle2 = 0.0
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1495
|
-
if(mm_angle12 == -0.0): mm_angle12 = 0.0
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1496
|
-
if(mm_angle21 == -0.0): mm_angle21 = 0.0
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1497
|
-
if (n_Lattice == 3):
|
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1498
|
-
if(var_A3 == -0.0): var_A3 = 0.0
|
|
1499
|
-
if(var_B3 == -0.0): var_B3 = 0.0
|
|
1500
|
-
if(var_Area3 == -0.0): var_Area3 = 0.0
|
|
1501
|
-
if(mm_Area13 == -0.0): mm_Area13 = 0.0
|
|
1502
|
-
if(mm_Area31 == -0.0): mm_Area31 = 0.0
|
|
1503
|
-
if(var_angle3 == -0.0): var_angle3 = 0.0
|
|
1504
|
-
if(mm_angle13 == -0.0): mm_angle13 = 0.0
|
|
1505
|
-
if(mm_angle31 == -0.0): mm_angle31 = 0.0
|
|
1506
|
-
#------------------------------------------
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|
1507
|
-
|
|
1508
|
-
#=====================================================
|
|
1509
|
-
# Obtenção das Matrizes de Strain para cada rede =====
|
|
1510
|
-
#=====================================================
|
|
1511
|
-
Lattice_A = [ [A1[0], A1[1]], [B1[0], B1[1]] ]
|
|
1512
|
-
Lattice_B = [ [A2_rotated[0], A2_rotated[1]], [B2_rotated[0], B2_rotated[1]] ]
|
|
1299
|
+
#----------------------------
|
|
1300
|
+
for j in range(2):
|
|
1301
|
+
VTemp1 = poscar1.readline()
|
|
1302
|
+
VTemp2 = poscar2.readline()
|
|
1303
|
+
if (n_Lattice == 3): VTemp3 = poscar3.readline()
|
|
1304
|
+
|
|
1305
|
+
#--------------------------------------------------------------------------------------------
|
|
1306
|
+
# Obtendo o módulo dos vetores (A,B), Area das Células e o Angulo de Abertura das células ---
|
|
1307
|
+
#--------------------------------------------------------------------------------------------
|
|
1308
|
+
mod_A1 = np.linalg.norm(A1)
|
|
1309
|
+
mod_B1 = np.linalg.norm(B1)
|
|
1310
|
+
mod_A2 = np.linalg.norm(A2)
|
|
1311
|
+
mod_B2 = np.linalg.norm(B2)
|
|
1312
|
+
Area1 = np.linalg.norm(np.cross(A1, B1))
|
|
1313
|
+
Area2 = np.linalg.norm(np.cross(A2, B2))
|
|
1314
|
+
angle_1 = np.arccos(np.dot(A1,B1)/(mod_A1*mod_B1))
|
|
1315
|
+
angle_2 = np.arccos(np.dot(A2,B2)/(mod_A2*mod_B2))
|
|
1316
|
+
if (n_Lattice == 3):
|
|
1317
|
+
mod_A3 = np.linalg.norm(A3)
|
|
1318
|
+
mod_B3 = np.linalg.norm(B3)
|
|
1319
|
+
Area3 = np.linalg.norm(np.cross(A3, B3))
|
|
1320
|
+
angle_3 = np.arccos(np.dot(A3,B3)/(mod_A3*mod_B3))
|
|
1321
|
+
|
|
1322
|
+
#----------------------------------------------------------------------------------------------------------------
|
|
1323
|
+
# Alinhando as células das diferemtes redes ---------------------------------------------------------------------
|
|
1324
|
+
#----------------------------------------------------------------------------------------------------------------
|
|
1325
|
+
theta = angle_V12; rotation_matrix = np.array([[np.cos(theta), -np.sin(theta)], [np.sin(theta), np.cos(theta)]])
|
|
1326
|
+
A2_rotated = np.dot(rotation_matrix, A2)
|
|
1327
|
+
B2_rotated = np.dot(rotation_matrix, B2)
|
|
1328
|
+
#---------------------------------------
|
|
1329
|
+
if (n_Lattice == 3):
|
|
1330
|
+
theta = angle_V13; rotation_matrix = np.array([[np.cos(theta), -np.sin(theta)], [np.sin(theta), np.cos(theta)]])
|
|
1331
|
+
A3_rotated = np.dot(rotation_matrix, A3)
|
|
1332
|
+
B3_rotated = np.dot(rotation_matrix, B3)
|
|
1333
|
+
#-------------------------------------------------------
|
|
1334
|
+
# Definindo a célula intermediária ---------------------
|
|
1335
|
+
#-------------------------------------------------------
|
|
1336
|
+
if (mismatch_type == 0):
|
|
1337
|
+
if (n_Lattice == 2):
|
|
1338
|
+
A_int = (A1 + A2_rotated)/2
|
|
1339
|
+
B_int = (B1 + B2_rotated)/2
|
|
1513
1340
|
if (n_Lattice == 3):
|
|
1514
|
-
|
|
1515
|
-
|
|
1516
|
-
|
|
1517
|
-
|
|
1518
|
-
|
|
1519
|
-
|
|
1520
|
-
|
|
1521
|
-
|
|
1522
|
-
|
|
1523
|
-
|
|
1524
|
-
|
|
1525
|
-
|
|
1526
|
-
|
|
1527
|
-
|
|
1528
|
-
|
|
1529
|
-
|
|
1530
|
-
|
|
1531
|
-
|
|
1532
|
-
|
|
1341
|
+
A_int = (A1 + A2_rotated + A3_rotated)/3
|
|
1342
|
+
B_int = (B1 + B2_rotated + B3_rotated)/3
|
|
1343
|
+
#---------------------------------------------
|
|
1344
|
+
if (mismatch_type == 1):
|
|
1345
|
+
A_int = A1
|
|
1346
|
+
B_int = B1
|
|
1347
|
+
#-----------------------
|
|
1348
|
+
if (mismatch_type == 2):
|
|
1349
|
+
A_int = A2_rotated
|
|
1350
|
+
B_int = B2_rotated
|
|
1351
|
+
#-----------------------
|
|
1352
|
+
if (mismatch_type == 3):
|
|
1353
|
+
A_int = A3_rotated
|
|
1354
|
+
B_int = B3_rotated
|
|
1355
|
+
#--------------------------------
|
|
1356
|
+
mod_A_int = np.linalg.norm(A_int)
|
|
1357
|
+
mod_B_int = np.linalg.norm(B_int)
|
|
1358
|
+
Area_int = np.linalg.norm(np.cross(A_int, B_int))
|
|
1359
|
+
angle_int = np.arctan2(np.cross(A_int,B_int), np.dot(A_int,B_int))
|
|
1360
|
+
|
|
1361
|
+
#------------------------------------------------------------------------------------------------------------------------
|
|
1362
|
+
# Utilização de vetores temporários (A,B) a fim de estimar a deformação sofrida pelas células originais -----------------
|
|
1363
|
+
#------------------------------------------------------------------------------------------------------------------------
|
|
1364
|
+
var_A1 = ((mod_A_int -mod_A1)/mod_A1)*100; var_A1 = round(var_A1, 4)
|
|
1365
|
+
var_B1 = ((mod_B_int -mod_B1)/mod_B1)*100; var_B1 = round(var_B1, 4)
|
|
1366
|
+
var_A2 = ((mod_A_int -mod_A2)/mod_A2)*100; var_A2 = round(var_A2, 4)
|
|
1367
|
+
var_B2 = ((mod_B_int -mod_B2)/mod_B2)*100; var_B2 = round(var_B2, 4)
|
|
1368
|
+
if (n_Lattice == 3):
|
|
1369
|
+
var_A3 = ((mod_A_int -mod_A3)/mod_A3)*100; var_A3 = round(var_A3, 4)
|
|
1370
|
+
var_B3 = ((mod_B_int -mod_B3)/mod_B3)*100; var_B3 = round(var_B3, 4)
|
|
1371
|
+
#--------------------------------------------------------------------------------
|
|
1372
|
+
mm_angle12 = ((angle_2 -angle_1)/angle_1)*100; mm_angle12 = round(mm_angle12, 4)
|
|
1373
|
+
mm_angle21 = ((angle_1 -angle_2)/angle_2)*100; mm_angle21 = round(mm_angle21, 4)
|
|
1374
|
+
if (n_Lattice == 3):
|
|
1375
|
+
mm_angle13 = ((angle_3 -angle_1)/angle_1)*100; mm_angle13 = round(mm_angle13, 4)
|
|
1376
|
+
mm_angle31 = ((angle_1 -angle_3)/angle_3)*100; mm_angle31 = round(mm_angle31, 4)
|
|
1377
|
+
#-----------------------------------------------------------------------------------
|
|
1378
|
+
var_angle1 = ((angle_int -angle_1)/angle_1)*100; var_angle1 = round(var_angle1, 4)
|
|
1379
|
+
var_angle2 = ((angle_int -angle_2)/angle_2)*100; var_angle2 = round(var_angle2, 4)
|
|
1380
|
+
if (n_Lattice == 3):
|
|
1381
|
+
var_angle3 = ((angle_int -angle_3)/angle_3)*100; var_angle3 = round(var_angle3, 4)
|
|
1382
|
+
#-------------------------------------------------------------------------------------
|
|
1383
|
+
mm_Area12 = ((Area2 -Area1)/Area1)*100; mm_Area12 = round(mm_Area12, 4)
|
|
1384
|
+
mm_Area21 = ((Area1 -Area2)/Area2)*100; mm_Area21 = round(mm_Area21, 4)
|
|
1385
|
+
if (n_Lattice == 3):
|
|
1386
|
+
mm_Area13 = ((Area3 -Area1)/Area1)*100; mm_Area13 = round(mm_Area13, 4)
|
|
1387
|
+
mm_Area31 = ((Area1 -Area3)/Area3)*100; mm_Area31 = round(mm_Area31, 4)
|
|
1388
|
+
#--------------------------------------------------------------------------
|
|
1389
|
+
var_Area1 = ((Area_int -Area1)/Area1)*100; var_Area1 = round(var_Area1, 4)
|
|
1390
|
+
var_Area2 = ((Area_int -Area2)/Area2)*100; var_Area2 = round(var_Area2, 4)
|
|
1391
|
+
if (n_Lattice == 3):
|
|
1392
|
+
var_Area3 = ((Area_int -Area3)/Area3)*100; var_Area3 = round(var_Area3, 4)
|
|
1393
|
+
#-----------------------------------------------------------------------------
|
|
1394
|
+
if(var_A1 == -0.0): var_A1 = 0.0
|
|
1395
|
+
if(var_B1 == -0.0): var_B1 = 0.0
|
|
1396
|
+
if(var_A2 == -0.0): var_A2 = 0.0
|
|
1397
|
+
if(var_B2 == -0.0): var_B2 = 0.0
|
|
1398
|
+
if(var_Area1 == -0.0): var_Area1 = 0.0
|
|
1399
|
+
if(var_Area2 == -0.0): var_Area2 = 0.0
|
|
1400
|
+
if(mm_Area12 == -0.0): mm_Area12 = 0.0
|
|
1401
|
+
if(mm_Area21 == -0.0): mm_Area21 = 0.0
|
|
1402
|
+
if(var_angle1 == -0.0): var_angle1 = 0.0
|
|
1403
|
+
if(var_angle2 == -0.0): var_angle2 = 0.0
|
|
1404
|
+
if(mm_angle12 == -0.0): mm_angle12 = 0.0
|
|
1405
|
+
if(mm_angle21 == -0.0): mm_angle21 = 0.0
|
|
1406
|
+
if (n_Lattice == 3):
|
|
1407
|
+
if(var_A3 == -0.0): var_A3 = 0.0
|
|
1408
|
+
if(var_B3 == -0.0): var_B3 = 0.0
|
|
1409
|
+
if(var_Area3 == -0.0): var_Area3 = 0.0
|
|
1410
|
+
if(mm_Area13 == -0.0): mm_Area13 = 0.0
|
|
1411
|
+
if(mm_Area31 == -0.0): mm_Area31 = 0.0
|
|
1412
|
+
if(var_angle3 == -0.0): var_angle3 = 0.0
|
|
1413
|
+
if(mm_angle13 == -0.0): mm_angle13 = 0.0
|
|
1414
|
+
if(mm_angle31 == -0.0): mm_angle31 = 0.0
|
|
1415
|
+
#------------------------------------------
|
|
1416
|
+
|
|
1417
|
+
#=====================================================
|
|
1418
|
+
# Obtenção das Matrizes de Strain para cada rede =====
|
|
1419
|
+
#=====================================================
|
|
1420
|
+
Lattice_A = [ [A1[0], A1[1]], [B1[0], B1[1]] ]
|
|
1421
|
+
Lattice_B = [ [A2_rotated[0], A2_rotated[1]], [B2_rotated[0], B2_rotated[1]] ]
|
|
1422
|
+
if (n_Lattice == 3):
|
|
1423
|
+
Lattice_C = [ [A3_rotated[0], A3_rotated[1]], [B3_rotated[0], B3_rotated[1]] ]
|
|
1424
|
+
Lattice_D = [ [A_int[0], A_int[1]], [B_int[0], B_int[1]] ]
|
|
1425
|
+
#---------------------------------------------------------
|
|
1426
|
+
I = np.eye(2)
|
|
1427
|
+
Lattice_A_inv = np.linalg.inv(Lattice_A)
|
|
1428
|
+
F_A = np.dot(Lattice_D, Lattice_A_inv)
|
|
1429
|
+
MStrain_A = 0.5 * (np.dot(F_A.T, F_A) - I)
|
|
1430
|
+
for aa in range(2):
|
|
1431
|
+
for bb in range(2):
|
|
1432
|
+
#----------------------------------
|
|
1433
|
+
F_A[aa][bb] = round(F_A[aa][bb], 9)
|
|
1434
|
+
MStrain_A[aa][bb] = round(MStrain_A[aa][bb], 9)
|
|
1435
|
+
#----------------------------------------------
|
|
1436
|
+
if (F_A[aa][bb] == -0.0): F_A[aa][bb] = 0.0
|
|
1437
|
+
if (MStrain_A[aa][bb] == -0.0): MStrain_A[aa][bb] = 0.0
|
|
1438
|
+
#--------------------------------------------------------------
|
|
1439
|
+
Lattice_B_inv = np.linalg.inv(Lattice_B)
|
|
1440
|
+
F_B = np.dot(Lattice_D, Lattice_B_inv)
|
|
1441
|
+
MStrain_B = 0.5 * (np.dot(F_B.T, F_B) - I)
|
|
1442
|
+
for aa in range(2):
|
|
1443
|
+
for bb in range(2):
|
|
1444
|
+
#----------------------------------
|
|
1445
|
+
F_B[aa][bb] = round(F_B[aa][bb], 9)
|
|
1446
|
+
MStrain_B[aa][bb] = round(MStrain_B[aa][bb], 9)
|
|
1447
|
+
#----------------------------------------------
|
|
1448
|
+
if (F_B[aa][bb] == -0.0): F_B[aa][bb] = 0.0
|
|
1449
|
+
if (MStrain_B[aa][bb] == -0.0): MStrain_B[aa][bb] = 0.0
|
|
1450
|
+
#--------------------------------------------------------------
|
|
1451
|
+
if (n_Lattice == 3):
|
|
1452
|
+
Lattice_C_inv = np.linalg.inv(Lattice_C)
|
|
1453
|
+
F_C = np.dot(Lattice_D, Lattice_C_inv)
|
|
1454
|
+
MStrain_C = 0.5 * (np.dot(F_C.T, F_C) - I)
|
|
1533
1455
|
for aa in range(2):
|
|
1534
1456
|
for bb in range(2):
|
|
1535
1457
|
#----------------------------------
|
|
1536
|
-
|
|
1537
|
-
|
|
1458
|
+
F_C[aa][bb] = round(F_C[aa][bb], 9)
|
|
1459
|
+
MStrain_C[aa][bb] = round(MStrain_C[aa][bb], 9)
|
|
1538
1460
|
#----------------------------------------------
|
|
1539
|
-
if (
|
|
1540
|
-
if (
|
|
1541
|
-
|
|
1542
|
-
|
|
1543
|
-
|
|
1544
|
-
|
|
1545
|
-
|
|
1546
|
-
|
|
1547
|
-
|
|
1548
|
-
|
|
1549
|
-
|
|
1550
|
-
|
|
1551
|
-
|
|
1552
|
-
|
|
1553
|
-
if (MStrain_C[aa][bb] == -0.0): MStrain_C[aa][bb] = 0.0
|
|
1554
|
-
|
|
1555
|
-
|
|
1556
|
-
poscar_new.write(f'SAMBA {label_htstructure} {nions_1} {nions_2}')
|
|
1557
|
-
if (n_Lattice == 3): poscar_new.write(f' {nions_3}')
|
|
1558
|
-
#---------------------------------------------------
|
|
1559
|
-
if (n_Lattice == 2):
|
|
1560
|
-
poscar_new.write(f' | mismatch_areas_12_21 = {mm_Area12}_{mm_Area21}')
|
|
1561
|
-
poscar_new.write(f' | var_areas = {var_Area1}_{var_Area2}')
|
|
1562
|
-
poscar_new.write(f' | var_vectors = {var_A1}_{var_B1}_{var_A2}_{var_B2}')
|
|
1563
|
-
poscar_new.write(f' | mismatch_angles_12_21 = {mm_angle12}_{mm_angle21}')
|
|
1564
|
-
poscar_new.write(f' | var_angles = {var_angle1}_{var_angle2}')
|
|
1565
|
-
poscar_new.write(f' | rotation_angle = {angle1}')
|
|
1566
|
-
if (n_Lattice == 3):
|
|
1567
|
-
poscar_new.write(f' | mismatch_Areas_12_21_13_31 = {mm_Area12}_{mm_Area21}_{mm_Area13}_{mm_Area31}')
|
|
1568
|
-
poscar_new.write(f' | var_Areas = {var_Area1}_{var_Area2}_{var_Area3}')
|
|
1569
|
-
poscar_new.write(f' | var_vectors = {var_A1}_{var_B1}_{var_A2}_{var_B2}_{var_A3}_{var_B3}')
|
|
1570
|
-
poscar_new.write(f' | mismatch_angles_12_21_13_31 = {mm_angle12}_{mm_angle21}_{mm_angle13}_{mm_angle31}')
|
|
1571
|
-
poscar_new.write(f' | var_angles = {var_angle1}_{var_angle2}_{var_angle3}')
|
|
1572
|
-
poscar_new.write(f' | rotation_angle = {angle1}_{angle3}')
|
|
1573
|
-
#------------------------------------------------------------
|
|
1574
|
-
poscar_new.write(f' | MSCell_1 = {int(MT1_00[i])}_{int(MT1_01[i])}_{int(MT1_10[i])}_{int(MT1_10[i])}')
|
|
1575
|
-
poscar_new.write(f' | MSCell_2 = {int(MT2_00[i])}_{int(MT2_01[i])}_{int(MT2_10[i])}_{int(MT2_10[i])}')
|
|
1576
|
-
if (n_Lattice == 3):
|
|
1577
|
-
poscar_new.write(f' | MSCell_3 = {int(MT3_00[i])}_{int(MT3_01[i])}_{int(MT3_10[i])}_{int(MT3_10[i])}')
|
|
1578
|
-
#----------------------------------------------
|
|
1579
|
-
poscar_new.write(f' | MDeform_1 = {float(F_A[0][0])}_{float(F_A[0][1])}_{float(F_A[1][0])}_{float(F_A[1][1])}')
|
|
1580
|
-
poscar_new.write(f' | MDeform_2 = {float(F_B[0][0])}_{float(F_B[0][1])}_{float(F_B[1][0])}_{float(F_B[1][1])}')
|
|
1581
|
-
if (n_Lattice == 3):
|
|
1582
|
-
poscar_new.write(f' | MDeform_3 = {float(F_C[0][0])}_{float(F_C[0][1])}_{float(F_C[1][0])}_{float(F_C[1][1])}')
|
|
1583
|
-
#----------------------------------------------
|
|
1584
|
-
poscar_new.write(f' | MSTrain_1 = {float(MStrain_A[0][0])}_{float(MStrain_A[0][1])}_{float(MStrain_A[1][0])}_{float(MStrain_A[1][1])}')
|
|
1585
|
-
poscar_new.write(f' | MSTrain_2 = {float(MStrain_B[0][0])}_{float(MStrain_B[0][1])}_{float(MStrain_B[1][0])}_{float(MStrain_B[1][1])}')
|
|
1586
|
-
if (n_Lattice == 3):
|
|
1587
|
-
poscar_new.write(f' | MSTrain_3 = {float(MStrain_C[0][0])}_{float(MStrain_C[0][1])}_{float(MStrain_C[1][0])}_{float(MStrain_C[1][1])}')
|
|
1588
|
-
#--------------------------------------------
|
|
1589
|
-
if (n_Lattice == 2):
|
|
1590
|
-
poscar_new.write(f' | Shift_plane = 0.0_0.0')
|
|
1591
|
-
if (n_Lattice == 3):
|
|
1592
|
-
poscar_new.write(f' | Shift_plane = 0.0_0.0_0.0_0.0')
|
|
1593
|
-
#----------------------------------------------
|
|
1594
|
-
poscar_new.write(f' | {ID_Heteroestrutura} \n')
|
|
1595
|
-
#----------------------------------------------
|
|
1596
|
-
poscar_new.write(f'1.0 \n')
|
|
1597
|
-
poscar_new.write(f'{A_int[0]} {A_int[1]} 0.0 \n')
|
|
1598
|
-
poscar_new.write(f'{B_int[0]} {B_int[1]} 0.0 \n')
|
|
1599
|
-
|
|
1600
|
-
VTemp1 = poscar1.readline().split()
|
|
1601
|
-
VTemp2 = poscar2.readline()
|
|
1602
|
-
if (n_Lattice == 3): VTemp3 = poscar3.readline()
|
|
1603
|
-
poscar_new.write(f'{VTemp1[0]} {VTemp1[1]} {VTemp1[2]} \n')
|
|
1604
|
-
|
|
1605
|
-
#=================================================================
|
|
1606
|
-
VTemp1 = poscar1.readline().split()
|
|
1607
|
-
VTemp2 = poscar2.readline().split()
|
|
1608
|
-
if (n_Lattice == 3): VTemp3 = poscar3.readline().split()
|
|
1609
|
-
for j in range(len(VTemp1)): poscar_new.write(f'{str(VTemp1[j])} ')
|
|
1610
|
-
for j in range(len(VTemp2)): poscar_new.write(f'{str(VTemp2[j])} ')
|
|
1461
|
+
if (F_C[aa][bb] == -0.0): F_C[aa][bb] = 0.0
|
|
1462
|
+
if (MStrain_C[aa][bb] == -0.0): MStrain_C[aa][bb] = 0.0
|
|
1463
|
+
|
|
1464
|
+
|
|
1465
|
+
poscar_new.write(f'SAMBA {label_htstructure} {nions_1} {nions_2}')
|
|
1466
|
+
if (n_Lattice == 3): poscar_new.write(f' {nions_3}')
|
|
1467
|
+
#---------------------------------------------------
|
|
1468
|
+
if (n_Lattice == 2):
|
|
1469
|
+
poscar_new.write(f' | mismatch_areas_12_21 = {mm_Area12}_{mm_Area21}')
|
|
1470
|
+
poscar_new.write(f' | var_areas = {var_Area1}_{var_Area2}')
|
|
1471
|
+
poscar_new.write(f' | var_vectors = {var_A1}_{var_B1}_{var_A2}_{var_B2}')
|
|
1472
|
+
poscar_new.write(f' | mismatch_angles_12_21 = {mm_angle12}_{mm_angle21}')
|
|
1473
|
+
poscar_new.write(f' | var_angles = {var_angle1}_{var_angle2}')
|
|
1474
|
+
poscar_new.write(f' | rotation_angle = {angle1}')
|
|
1611
1475
|
if (n_Lattice == 3):
|
|
1612
|
-
|
|
1613
|
-
|
|
1614
|
-
|
|
1615
|
-
|
|
1616
|
-
|
|
1617
|
-
|
|
1618
|
-
|
|
1619
|
-
|
|
1476
|
+
poscar_new.write(f' | mismatch_Areas_12_21_13_31 = {mm_Area12}_{mm_Area21}_{mm_Area13}_{mm_Area31}')
|
|
1477
|
+
poscar_new.write(f' | var_Areas = {var_Area1}_{var_Area2}_{var_Area3}')
|
|
1478
|
+
poscar_new.write(f' | var_vectors = {var_A1}_{var_B1}_{var_A2}_{var_B2}_{var_A3}_{var_B3}')
|
|
1479
|
+
poscar_new.write(f' | mismatch_angles_12_21_13_31 = {mm_angle12}_{mm_angle21}_{mm_angle13}_{mm_angle31}')
|
|
1480
|
+
poscar_new.write(f' | var_angles = {var_angle1}_{var_angle2}_{var_angle3}')
|
|
1481
|
+
poscar_new.write(f' | rotation_angle = {angle1}_{angle3}')
|
|
1482
|
+
#------------------------------------------------------------
|
|
1483
|
+
poscar_new.write(f' | MSCell_1 = {int(MT1_00[i])}_{int(MT1_01[i])}_{int(MT1_10[i])}_{int(MT1_10[i])}')
|
|
1484
|
+
poscar_new.write(f' | MSCell_2 = {int(MT2_00[i])}_{int(MT2_01[i])}_{int(MT2_10[i])}_{int(MT2_10[i])}')
|
|
1620
1485
|
if (n_Lattice == 3):
|
|
1621
|
-
|
|
1622
|
-
|
|
1623
|
-
|
|
1624
|
-
|
|
1486
|
+
poscar_new.write(f' | MSCell_3 = {int(MT3_00[i])}_{int(MT3_01[i])}_{int(MT3_10[i])}_{int(MT3_10[i])}')
|
|
1487
|
+
#----------------------------------------------
|
|
1488
|
+
poscar_new.write(f' | MDeform_1 = {float(F_A[0][0])}_{float(F_A[0][1])}_{float(F_A[1][0])}_{float(F_A[1][1])}')
|
|
1489
|
+
poscar_new.write(f' | MDeform_2 = {float(F_B[0][0])}_{float(F_B[0][1])}_{float(F_B[1][0])}_{float(F_B[1][1])}')
|
|
1490
|
+
if (n_Lattice == 3):
|
|
1491
|
+
poscar_new.write(f' | MDeform_3 = {float(F_C[0][0])}_{float(F_C[0][1])}_{float(F_C[1][0])}_{float(F_C[1][1])}')
|
|
1492
|
+
#----------------------------------------------
|
|
1493
|
+
poscar_new.write(f' | MSTrain_1 = {float(MStrain_A[0][0])}_{float(MStrain_A[0][1])}_{float(MStrain_A[1][0])}_{float(MStrain_A[1][1])}')
|
|
1494
|
+
poscar_new.write(f' | MSTrain_2 = {float(MStrain_B[0][0])}_{float(MStrain_B[0][1])}_{float(MStrain_B[1][0])}_{float(MStrain_B[1][1])}')
|
|
1495
|
+
if (n_Lattice == 3):
|
|
1496
|
+
poscar_new.write(f' | MSTrain_3 = {float(MStrain_C[0][0])}_{float(MStrain_C[0][1])}_{float(MStrain_C[1][0])}_{float(MStrain_C[1][1])}')
|
|
1497
|
+
#--------------------------------------------
|
|
1498
|
+
if (n_Lattice == 2):
|
|
1499
|
+
poscar_new.write(f' | Shift_plane = 0.0_0.0')
|
|
1500
|
+
if (n_Lattice == 3):
|
|
1501
|
+
poscar_new.write(f' | Shift_plane = 0.0_0.0_0.0_0.0')
|
|
1502
|
+
#----------------------------------------------
|
|
1503
|
+
poscar_new.write(f' | {ID_Heteroestrutura} \n')
|
|
1504
|
+
#----------------------------------------------
|
|
1505
|
+
poscar_new.write(f'1.0 \n')
|
|
1506
|
+
poscar_new.write(f'{A_int[0]} {A_int[1]} 0.0 \n')
|
|
1507
|
+
poscar_new.write(f'{B_int[0]} {B_int[1]} 0.0 \n')
|
|
1508
|
+
|
|
1509
|
+
VTemp1 = poscar1.readline().split()
|
|
1625
1510
|
VTemp2 = poscar2.readline()
|
|
1626
|
-
if (n_Lattice == 3):
|
|
1627
|
-
poscar_new.write(f'
|
|
1628
|
-
#-----------------------------
|
|
1629
|
-
for j in range(nions_1):
|
|
1630
|
-
VTemp1 = poscar1.readline().split()
|
|
1631
|
-
Z1 = ((vacuum/2)/d)
|
|
1632
|
-
poscar_new.write(f'{float(VTemp1[0])} {float(VTemp1[1])} {Z1 + float(VTemp1[2])} \n')
|
|
1633
|
-
for j in range(nions_2):
|
|
1634
|
-
VTemp2 = poscar2.readline().split()
|
|
1635
|
-
Z2 = Z1 + ((dZ[0] + separacao1)/d)
|
|
1636
|
-
poscar_new.write(f'{float(VTemp2[0])} {float(VTemp2[1])} {Z2 + float(VTemp2[2])} \n')
|
|
1637
|
-
if (n_Lattice == 3):
|
|
1638
|
-
for j in range(nions_3):
|
|
1639
|
-
VTemp3 = poscar3.readline().split()
|
|
1640
|
-
Z3 = Z2 + ((dZ[1] + separacao2)/d)
|
|
1641
|
-
poscar_new.write(f'{float(VTemp3[0])} {float(VTemp3[1])} {Z3 + float(VTemp3[2])} \n')
|
|
1642
|
-
#-------------------------------------------------------------------------------------------
|
|
1643
|
-
poscar1.close()
|
|
1644
|
-
poscar2.close()
|
|
1645
|
-
if (n_Lattice == 3): poscar3.close()
|
|
1646
|
-
poscar_new.close()
|
|
1647
|
-
#-----------------
|
|
1511
|
+
if (n_Lattice == 3): VTemp3 = poscar3.readline()
|
|
1512
|
+
poscar_new.write(f'{VTemp1[0]} {VTemp1[1]} {VTemp1[2]} \n')
|
|
1648
1513
|
|
|
1649
|
-
|
|
1650
|
-
|
|
1651
|
-
|
|
1652
|
-
|
|
1653
|
-
|
|
1654
|
-
|
|
1655
|
-
|
|
1656
|
-
|
|
1657
|
-
|
|
1658
|
-
|
|
1514
|
+
#=================================================================
|
|
1515
|
+
VTemp1 = poscar1.readline().split()
|
|
1516
|
+
VTemp2 = poscar2.readline().split()
|
|
1517
|
+
if (n_Lattice == 3): VTemp3 = poscar3.readline().split()
|
|
1518
|
+
for j in range(len(VTemp1)): poscar_new.write(f'{str(VTemp1[j])} ')
|
|
1519
|
+
for j in range(len(VTemp2)): poscar_new.write(f'{str(VTemp2[j])} ')
|
|
1520
|
+
if (n_Lattice == 3):
|
|
1521
|
+
for j in range(len(VTemp3)): poscar_new.write(f'{str(VTemp3[j])} ')
|
|
1522
|
+
poscar_new.write(f' \n')
|
|
1523
|
+
#---------------------------------------------------------------------
|
|
1524
|
+
VTemp1 = poscar1.readline().split()
|
|
1525
|
+
VTemp2 = poscar2.readline().split()
|
|
1526
|
+
if (n_Lattice == 3): VTemp3 = poscar3.readline().split()
|
|
1527
|
+
for j in range(len(VTemp1)): poscar_new.write(f'{str(VTemp1[j])} ')
|
|
1528
|
+
for j in range(len(VTemp2)): poscar_new.write(f'{str(VTemp2[j])} ')
|
|
1529
|
+
if (n_Lattice == 3):
|
|
1530
|
+
for j in range(len(VTemp3)): poscar_new.write(f'{str(VTemp3[j])} ')
|
|
1531
|
+
poscar_new.write(f' \n')
|
|
1532
|
+
#---------------------------------------------------------------------
|
|
1533
|
+
VTemp1 = poscar1.readline()
|
|
1534
|
+
VTemp2 = poscar2.readline()
|
|
1535
|
+
if (n_Lattice == 3): VTemp3 = poscar3.readline()
|
|
1536
|
+
poscar_new.write(f'direct \n')
|
|
1537
|
+
#-----------------------------
|
|
1538
|
+
for j in range(nions_1):
|
|
1539
|
+
VTemp1 = poscar1.readline().split()
|
|
1540
|
+
Z1 = ((vacuum/2)/d)
|
|
1541
|
+
poscar_new.write(f'{float(VTemp1[0])} {float(VTemp1[1])} {Z1 + float(VTemp1[2])} \n')
|
|
1542
|
+
for j in range(nions_2):
|
|
1543
|
+
VTemp2 = poscar2.readline().split()
|
|
1544
|
+
Z2 = Z1 + ((dZ[0] + separacao1)/d)
|
|
1545
|
+
poscar_new.write(f'{float(VTemp2[0])} {float(VTemp2[1])} {Z2 + float(VTemp2[2])} \n')
|
|
1546
|
+
if (n_Lattice == 3):
|
|
1547
|
+
for j in range(nions_3):
|
|
1548
|
+
VTemp3 = poscar3.readline().split()
|
|
1549
|
+
Z3 = Z2 + ((dZ[1] + separacao2)/d)
|
|
1550
|
+
poscar_new.write(f'{float(VTemp3[0])} {float(VTemp3[1])} {Z3 + float(VTemp3[2])} \n')
|
|
1551
|
+
#-------------------------------------------------------------------------------------------
|
|
1552
|
+
poscar1.close()
|
|
1553
|
+
poscar2.close()
|
|
1554
|
+
if (n_Lattice == 3): poscar3.close()
|
|
1555
|
+
poscar_new.close()
|
|
1556
|
+
#-----------------
|
|
1557
|
+
|
|
1558
|
+
#--------------------------------------------------------------
|
|
1559
|
+
# Excluindo Heteroestrutura distorcida ------------------------
|
|
1560
|
+
#--------------------------------------------------------------
|
|
1561
|
+
dist_3 = 0.0
|
|
1562
|
+
dist_1 = abs(var_A1 -var_B1)
|
|
1563
|
+
dist_2 = abs(var_A2 -var_B2)
|
|
1564
|
+
if (n_Lattice == 3): dist_3 = abs(var_A3 -var_B3)
|
|
1565
|
+
#----------------------------------------------------------------------------------------------------
|
|
1566
|
+
if (dist_1 > crit_distorc_lattice or dist_2 > crit_distorc_lattice or dist_3 > crit_distorc_lattice):
|
|
1567
|
+
os.remove(diret2 + dir_temp_m + '/POSCAR_' + str(i+1) + '.vasp')
|
|
1659
1568
|
|
|
1660
1569
|
|
|
1661
1570
|
#=====================================================================
|
|
@@ -1841,15 +1750,7 @@ for s in range(len(files0)):
|
|
|
1841
1750
|
#-----------------
|
|
1842
1751
|
if (dAB1 == dAB2):
|
|
1843
1752
|
cont = 1
|
|
1844
|
-
|
|
1845
|
-
if ( (Angle_AB1 < 0) and (Angle_AB2 > 0) and cont == 1 ):
|
|
1846
|
-
if os.path.exists(diret2 + files0[s] + '/' + files[i]):
|
|
1847
|
-
os.remove(diret2 + files0[s] + '/' + files[i])
|
|
1848
|
-
n_exclusion += 1; cont = 0
|
|
1849
|
-
if ( (Angle_AB1 > 0) and (Angle_AB2 < 0) and cont == 1 ):
|
|
1850
|
-
if os.path.exists(diret2 + files0[s] + '/' + files[j]):
|
|
1851
|
-
os.remove(diret2 + files0[s] + '/' + files[j])
|
|
1852
|
-
n_exclusion += 1; cont = 0
|
|
1753
|
+
#--------------------------------------------------
|
|
1853
1754
|
if (abs(Angle_AB1) < abs(Angle_AB2) and cont == 1):
|
|
1854
1755
|
if os.path.exists(diret2 + files0[s] + '/' + files[j]):
|
|
1855
1756
|
os.remove(diret2 + files0[s] + '/' + files[j])
|
|
@@ -1858,10 +1759,15 @@ for s in range(len(files0)):
|
|
|
1858
1759
|
if os.path.exists(diret2 + files0[s] + '/' + files[i]):
|
|
1859
1760
|
os.remove(diret2 + files0[s] + '/' + files[i])
|
|
1860
1761
|
n_exclusion += 1; cont = 0
|
|
1861
|
-
if (Angle_AB1 == Angle_AB2 and cont == 1):
|
|
1862
|
-
if
|
|
1863
|
-
os.
|
|
1864
|
-
|
|
1762
|
+
if (abs(Angle_AB1) == abs(Angle_AB2) and cont == 1):
|
|
1763
|
+
if (Angle_AB1 >= Angle_AB2):
|
|
1764
|
+
if os.path.exists(diret2 + files0[s] + '/' + files[j]):
|
|
1765
|
+
os.remove(diret2 + files0[s] + '/' + files[j])
|
|
1766
|
+
n_exclusion += 1
|
|
1767
|
+
if (Angle_AB1 < Angle_AB2):
|
|
1768
|
+
if os.path.exists(diret2 + files0[s] + '/' + files[i]):
|
|
1769
|
+
os.remove(diret2 + files0[s] + '/' + files[i])
|
|
1770
|
+
n_exclusion += 1
|
|
1865
1771
|
|
|
1866
1772
|
#---------------
|
|
1867
1773
|
n_structures = 0
|
|
@@ -2059,15 +1965,7 @@ for i in range(len(files)):
|
|
|
2059
1965
|
#-----------------
|
|
2060
1966
|
if (dAB1 == dAB2):
|
|
2061
1967
|
cont = 1
|
|
2062
|
-
|
|
2063
|
-
if ( (Angle_AB1 < 0) and (Angle_AB2 > 0) and cont == 1 ):
|
|
2064
|
-
if os.path.exists(diret2 + files[i]):
|
|
2065
|
-
os.remove(diret2 + files[i])
|
|
2066
|
-
n_exclusion += 1; cont = 0
|
|
2067
|
-
if ( (Angle_AB1 > 0) and (Angle_AB2 < 0) and cont == 1 ):
|
|
2068
|
-
if os.path.exists(diret2 + files[j]):
|
|
2069
|
-
os.remove(diret2 + files[j])
|
|
2070
|
-
n_exclusion += 1; cont = 0
|
|
1968
|
+
#--------------------------------------------------
|
|
2071
1969
|
if (abs(Angle_AB1) < abs(Angle_AB2) and cont == 1):
|
|
2072
1970
|
if os.path.exists(diret2 + files[j]):
|
|
2073
1971
|
os.remove(diret2 + files[j])
|
|
@@ -2076,10 +1974,15 @@ for i in range(len(files)):
|
|
|
2076
1974
|
if os.path.exists(diret2 + files[i]):
|
|
2077
1975
|
os.remove(diret2 + files[i])
|
|
2078
1976
|
n_exclusion += 1; cont = 0
|
|
2079
|
-
if (Angle_AB1 == Angle_AB2 and cont == 1):
|
|
2080
|
-
if
|
|
2081
|
-
os.
|
|
2082
|
-
|
|
1977
|
+
if (abs(Angle_AB1) == abs(Angle_AB2) and cont == 1):
|
|
1978
|
+
if (Angle_AB1 >= Angle_AB2):
|
|
1979
|
+
if os.path.exists(diret2 + files[j]):
|
|
1980
|
+
os.remove(diret2 + files[j])
|
|
1981
|
+
n_exclusion += 1
|
|
1982
|
+
if (Angle_AB1 < Angle_AB2):
|
|
1983
|
+
if os.path.exists(diret2 + files[i]):
|
|
1984
|
+
os.remove(diret2 + files[i])
|
|
1985
|
+
n_exclusion += 1
|
|
2083
1986
|
|
|
2084
1987
|
#-------------------------
|
|
2085
1988
|
files = os.listdir(diret2)
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/HeteroStructure_Generator_OLD_1.py
RENAMED
|
File without changes
|
{samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/HeteroStructure_Generator_OLD_2.py
RENAMED
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{samba_ilum-1.0.0.484 → samba_ilum-1.0.0.486}/samba_ilum/src/INPUTS/SAMBA_HeteroStructure.input
RENAMED
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|