style: utils package refactor

.gitignore

@@ -0,0 +1 @@
+__pycache__ 

src/scripts/n2_nanocrack.py

@@ -0,0 +1,91 @@
+
+from utils import read_xyz, write_xyz
+import sys
+sys.path.append('./src/utils')
+
+# Replicar a célula unitária com os nanocracks lineares (n2)
+
+
+def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size):
+    replicated_atoms = []
+    for i in range(n_replications_x):
+        for j in range(n_replications_y):
+            for index, (atom, position) in enumerate(atoms):
+                # POSICOES PERMANECEM CONSTANTES
+                new_position = [
+                    position[0] + (lattice_constants[0]) * i, position[1] + (lattice_constants[1])*j, 0.0]
+
+                if i == (n_replications_x // 2 - 1):  # meio - 1 (lateral left) (6)
+                    floor = int(n_replications_y//2 -
+                                ((crack_size - 1)/2) + 1)  # 5
+                    ceiling = int(n_replications_y//2 +
+                                  ((crack_size - 1)/2) - 1)  # 9
+                    if j in range(floor, ceiling+1):
+                        atom = 'H'
+                        if (j == floor and index in [0, 1, 2, 8, 9]) or (j == ceiling and index in [5, 6, 7, 8, 9]):
+                            replicated_atoms.append((atom, new_position))
+                        else:
+                            if index in [8, 9]:
+                                replicated_atoms.append((atom, new_position))
+                    else:
+                        replicated_atoms.append((atom, new_position))
+
+                elif i == (n_replications_x // 2):  # meio (7)
+                    floor = int(n_replications_y//2 -
+                                ((crack_size - 1)/2))  # 4
+                    ceiling = int(n_replications_y//2 +
+                                  ((crack_size - 1)/2))  # 10
+                    if j in range(floor, ceiling+1):
+                        atom = 'H'
+                        if (j == floor and index in [0, 1, 2, 3, 4, 8, 9]) or (j == ceiling and index in [3, 4, 5, 6, 7, 8, 9]):
+                            replicated_atoms.append((atom, new_position))
+                    else:
+                        replicated_atoms.append((atom, new_position))
+
+                elif i == (n_replications_x // 2 + 1):  # meio + 1 (lateral right) (8)
+                    floor = int(n_replications_y//2 -
+                                ((crack_size - 1)/2) + 1)  # 5
+                    ceiling = int(n_replications_y//2 +
+                                  ((crack_size - 1)/2) - 1)  # 9
+                    if j in range(floor, ceiling+1):
+                        atom = 'H'
+                        if (j == floor and index in [0, 1, 2, 3, 4]) or (j == ceiling and index in [3, 4, 5, 6, 7]):
+                            replicated_atoms.append((atom, new_position))
+                        else:
+                            if index in [3, 4]:
+                                replicated_atoms.append((atom, new_position))
+                    else:
+                        replicated_atoms.append((atom, new_position))
+                else:
+                    replicated_atoms.append((atom, new_position))
+    return [len(replicated_atoms), replicated_atoms]
+
+
+# Vetores de rede (lattice constants)
+a = 6.3028
+b = 4.9302
+lattice_constants = [a, b]
+
+# Parâmetros
+INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
+OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_nanocrack_structure.xyz'
+n_replications_x = 17
+n_replications_y = 17
+crack_size = 7
+
+OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_nanocrack_structure.xyz'
+
+# Ler a célula unitária
+n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
+
+# Replicar a célula unitária
+replicated_atoms = replicate_cell(
+    atoms, lattice_constants, n_replications_x, n_replications_y, crack_size)
+
+n_atoms_modified = replicated_atoms[0]
+atoms_modified = replicated_atoms[1]
+
+# Escrever o arquivo .xyz com a estrutura replicada
+write_xyz(OUTPUT_STRUCTURE_FILE, n_atoms_modified, comment, atoms_modified)
+
+print('Estrutura replicada, arquivo salvo em {}'.format(OUTPUT_STRUCTURE_FILE))

src/scripts/replicate_cell.py

@@ -1,13 +1,9 @@
 
-def read_xyz(file):
-    with open(file, 'r') as f:
-        n_atoms = int(f.readline())
-        comment = f.readline()
-        atoms = []
-        for line in f:
-            atom, x, y, z = line.split()
-            atoms.append((atom, [float(x), float(y), float(z)]))
-    return n_atoms, comment, atoms
+from utils import read_xyz, write_xyz
+import sys
+sys.path.append('./src/utils')
+
+# Replicar a célula unitária
 
 
 def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y):
@@ -21,17 +17,6 @@ def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y)
     return replicated_atoms
 
 
-def write_xyz(file, n_atoms, comment, atoms):
-    with open(file, 'w') as f:
-        f.write(str(n_atoms) + '\n')
-        f.write(comment)
-        for atom, position in atoms:
-            x = format(position[0], '.16f')
-            y = format(position[1], '.16f')
-            z = format(position[2], '.16f')
-            f.write('{} {} {} {}\n'.format(atom, x, y, z))
-
-
 # Vetores de rede (lattice constants)
 a = 6.3028
 b = 4.9302

src/utils/utils.py

@@ -0,0 +1,20 @@
+def read_xyz(file):
+    with open(file, 'r') as f:
+        n_atoms = int(f.readline())
+        comment = f.readline()
+        atoms = []
+        for line in f:
+            atom, x, y, z = line.split()
+            atoms.append((atom, [float(x), float(y), float(z)]))
+    return n_atoms, comment, atoms
+
+
+def write_xyz(file, n_atoms, comment, atoms):
+    with open(file, 'w') as f:
+        f.write(str(n_atoms) + '\n')
+        f.write(comment)
+        for atom, position in atoms:
+            x = format(position[0], '.16f')
+            y = format(position[1], '.16f')
+            z = format(position[2], '.16f')
+            f.write('{} {} {} {}\n'.format(atom, x, y, z))

tests/test.py

@@ -1,40 +0,0 @@
-import math
-
-hip = 1.42
-cateto = math.sqrt((hip**2) / 2)  # 1.0023
-
-a = 6.3028
-b = 4.9302
-x = (a - ((2*cateto) + (2*hip))) / 2  # 0.7238
-y = (b - (hip + (2*cateto))) / 2  # 0.75
-
-x1 = [x+cateto,                  y,                 0.0]
-x2 = [x+cateto+hip,              y,                 0.0]
-x3 = [x+cateto+(2*hip),          y,                 0.0]
-
-x4 = [x+(2*cateto)+(2*hip),      y+cateto,          0.0]
-x5 = [x+(2*cateto)+(2*hip),      y+cateto+hip,      0.0]
-
-x6 = [x+cateto+(2*hip),      y+(2*cateto)+hip,      0.0]
-x7 = [x+cateto+hip,          y+(2*cateto)+hip,      0.0]
-x8 = [x+cateto,              y+(2*cateto)+hip,      0.0]
-
-x9 = [x,                     y+cateto+hip,          0.0]
-x10 = [x,                     y+cateto,              0.0]
-
-
-def padraoAtomo(atomo):
-    x, y, z = atomo
-    x = format(x, '.16f')
-    y = format(y, '.16f')
-    z = format(z, '.16f')
-    return f"C       {x}       {y}       {z}"
-
-
-lista = [x1, x2, x3, x4, x5, x6, x7, x8, x9, x10]
-listaPadrao = [padraoAtomo(atomo) for atomo in lista]
-
-with open('tests/test.xyz', 'w') as file:
-    file.write(str(len(listaPadrao)) + '\n')
-    for atomo in listaPadrao:
-        file.write(atomo + '\n')