feat: bidirectional cracks

README.md

@@ -68,3 +68,26 @@ Acessar a pasta e executar o arquivo com a simulação do rasgo:
 ```
 python3 <nome_do_arquivo>.py
 ```
+
+## VMD Scripting 
+
+### set – Setting the unitcell parameters
+
+To be able to work correctly, all other procedures of the PBCTools plugin require the VMD unitcell parameters to be set. Some file formats and their readers provide the necessary information (e.g. the DCD, VTF and Amber crdbox formats). When the format does not provide the information, the parameters can either be set with help of the command pbc set, or they can be read in from a file in XST format via the procedure pbc readxst (see section 5).
+
+Syntax:
+
+```
+pbc set cell [options…]
+```
+Description
+
+Sets the VMD unit cell properties to cell in the specified frames. cell must either contain a single set of unit cell parameters that will be used in all frames of the molecule, or it must contain a parameter set for every frame.
+
+Example
+
+  Set the unit cell side length to 10 in all frames:
+
+  ```
+  pbc set {10.0 10.0 10.0}
+  ```

src/scripts/main.py

@@ -0,0 +1,16 @@
+
+import n1_crack
+import n2_crack
+import n1_edge_crack
+import replicate_cell
+
+if __name__ == "__main__":
+    print()
+    print("============================== Gerando Estruturas ==============================\n")
+    n1_crack.run('x')
+    n1_crack.run('y')
+    n1_edge_crack.run()
+    n2_crack.run('y')
+    replicate_cell.run()
+    print()
+    print("\033[1;32m" + "============================== Estruturas replicadas ===========================" + "\033[0m")

src/scripts/n1_crack.py

@@ -5,7 +5,7 @@
 
 
 # Replicar a célula unitária com os nanocracks lineares (n2)
-def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size,crack_direction):
+def replicate_n1_crack(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size,crack_direction):
     replicated_atoms = []
     for x in range(n_replications_x):
         for y in range(n_replications_y):
@@ -35,31 +35,39 @@ def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y,
 
     return [len(replicated_atoms), replicated_atoms]
 
+def run(crack_direction):
+    # Parâmetros
+    INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
 
-# Parâmetros
-INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
-OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_crack_structure.xyz'
-n_replications_x = 17
-n_replications_y = 19
-crack_size = 9
-crack_direction = 'y'
+    n_replications_x = 17
+    n_replications_y = 21
+    crack_size = 7
 
-# Ler a célula unitária
-n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
+    # Ler a célula unitária
+    n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
 
-# Vetores de rede (lattice constants)
-a = float(comment.split()[2])
-b = float(comment.split()[-2])
-lattice_constants = [a, b]
+    # Vetores de rede (lattice constants)
+    a = float(comment.split()[2])
+    b = float(comment.split()[-2])
+    lattice_constants = [a, b]
 
-# Replicar a célula unitária
-replicated_atoms = replicate_cell(
-    atoms, lattice_constants, n_replications_x, n_replications_y, crack_size,crack_direction)
+    # Replicar a célula unitária
 
-n_atoms_modified = replicated_atoms[0]
-atoms_modified = replicated_atoms[1]
+    replicated_atoms = replicate_n1_crack(
+        atoms, lattice_constants, n_replications_x, n_replications_y, crack_size,crack_direction)
 
-# Escrever o arquivo .xyz com a estrutura replicada
-write_xyz(OUTPUT_STRUCTURE_FILE, n_atoms_modified, comment, atoms_modified)
+    n_atoms_modified = replicated_atoms[0]
+    atoms_modified = replicated_atoms[1]
 
-print('Estrutura n1 replicada, arquivo salvo em {}'.format(OUTPUT_STRUCTURE_FILE))
+    # Escrever o arquivo .xyz com a estrutura replicada
+    if crack_size == 1:
+        OUTPUT_STRUCTURE_FILE = 'src/simulations/center_crack_structure.xyz'
+    elif crack_direction == 'x':
+        OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_x_crack_structure.xyz'
+    else:
+        OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_y_crack_structure.xyz'
+
+    write_xyz(OUTPUT_STRUCTURE_FILE, n_atoms_modified, comment, atoms_modified)
+
+
+    print('Estrutura com rasgo n1 replicada no eixo {}, arquivo salvo em {}'.format(crack_direction,OUTPUT_STRUCTURE_FILE))

src/scripts/n1_edge_crack.py

@@ -5,7 +5,7 @@
 
 
 # Replicar a célula unitária com os nanocracks lineares (n2)
-def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size):
+def replicate_edge_crack(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size):
     replicated_atoms = []
     for x in range(n_replications_x):
         for y in range(n_replications_y):
@@ -25,30 +25,30 @@ def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y,
 
     return [len(replicated_atoms), replicated_atoms]
 
+def run():
+    # Parâmetros
+    INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
+    OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_edge_crack_structure.xyz'
+    n_replications_x = 17
+    n_replications_y = 21
+    crack_size = 9
 
-# Parâmetros
-INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
-OUTPUT_STRUCTURE_FILE = 'src/simulations/n1_edge_crack_structure.xyz'
-n_replications_x = 17
-n_replications_y = 19
-crack_size = 9
+    # Ler a célula unitária
+    n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
 
-# Ler a célula unitária
-n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
+    # Vetores de rede (lattice constants)
+    a = float(comment.split()[2])
+    b = float(comment.split()[-2])
+    lattice_constants = [a, b]
 
-# Vetores de rede (lattice constants)
-a = float(comment.split()[2])
-b = float(comment.split()[-2])
-lattice_constants = [a, b]
+    # Replicar a célula unitária
+    replicated_atoms = replicate_edge_crack(
+        atoms, lattice_constants, n_replications_x, n_replications_y, crack_size)
 
-# 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]
 
-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)
 
-# Escrever o arquivo .xyz com a estrutura replicada
-write_xyz(OUTPUT_STRUCTURE_FILE, n_atoms_modified, comment, atoms_modified)
-
-print('Estrutura n1 replicada, arquivo salvo em {}'.format(OUTPUT_STRUCTURE_FILE))
+    print('Estrutura com rasgo em borda n1 replicada, arquivo salvo em {}'.format(OUTPUT_STRUCTURE_FILE))

src/scripts/n2_crack.py

@@ -4,7 +4,7 @@
 from n2_crack_utils import y_left_crack, y_center_crack, y_right_crack,x_left_crack, x_center_crack, x_right_crack
 
 # Replicar a célula unitária com os nanocracks lineares (n2)
-def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size):
+def replicate_n2_crack(atoms, lattice_constants, n_replications_x, n_replications_y, crack_size,crack_direction):
     replicated_atoms = []
     for x in range(n_replications_x):
         for y in range(n_replications_y):
@@ -56,31 +56,30 @@ def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y,
 
     return [len(replicated_atoms), replicated_atoms]
 
+def run(crack_direction):
+    # Parâmetros
+    INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
+    OUTPUT_STRUCTURE_FILE = 'src/simulations/n2_crack_structure.xyz'
+    n_replications_x = 17
+    n_replications_y = 21
+    crack_size = 9
 
-# Parâmetros
-INPUT_UNIT_CELL_FILE = 'src/simulations/unit_cell.xyz'
-OUTPUT_STRUCTURE_FILE = 'src/simulations/n2_crack_structure.xyz'
-n_replications_x = 17
-n_replications_y = 19
-crack_size = 9
-crack_direction = 'y'
+    # Ler a célula unitária
+    n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
 
-# Ler a célula unitária
-n_atoms, comment, atoms = read_xyz(INPUT_UNIT_CELL_FILE)
+    # Vetores de rede (lattice constants)
+    a = float(comment.split()[2])
+    b = float(comment.split()[-2])
+    lattice_constants = [a, b]
 
-# Vetores de rede (lattice constants)
-a = float(comment.split()[2])
-b = float(comment.split()[-2])
-lattice_constants = [a, b]
+    # Replicar a célula unitária
+    replicated_atoms = replicate_n2_crack(
+        atoms, lattice_constants, n_replications_x, n_replications_y, crack_size,crack_direction)
 
-# 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]
 
-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)
 
-# Escrever o arquivo .xyz com a estrutura replicada
-write_xyz(OUTPUT_STRUCTURE_FILE, n_atoms_modified, comment, atoms_modified)
-
-print('Estrutura n2 replicada, arquivo salvo em {}'.format(OUTPUT_STRUCTURE_FILE))
+    print('Estrutura com rasgo n2 replicada, arquivo salvo em {}'.format(OUTPUT_STRUCTURE_FILE))

src/scripts/replicate_cell.py

@@ -17,29 +17,29 @@ def replicate_cell(atoms, lattice_constants, n_replications_x, n_replications_y)
                 replicated_atoms.append((atom, new_position))
     return replicated_atoms
 
+def run():
+    # Parâmetros
+    unit_cell_file = 'src/simulations/unit_cell.xyz'
+    n_replications_x = 17
+    n_replications_y = 21
 
-# Parâmetros
-unit_cell_file = 'src/simulations/unit_cell.xyz'
-n_replications_x = 15
-n_replications_y = 15
+    # Ler a célula unitária
+    n_atoms, comment, atoms = read_xyz(unit_cell_file)
 
-# Ler a célula unitária
-n_atoms, comment, atoms = read_xyz(unit_cell_file)
+    # Vetores de rede (lattice constants)
+    a = float(comment.split()[2])
+    b = float(comment.split()[-2])
+    lattice_constants = [a, b]
 
-# Vetores de rede (lattice constants)
-a = float(comment.split()[2])
-b = float(comment.split()[-2])
-lattice_constants = [a, b]
+    # Replicar a célula unitária
+    replicated_atoms = replicate_cell(
+        atoms, lattice_constants, n_replications_x, n_replications_y)
 
-# Replicar a célula unitária
-replicated_atoms = replicate_cell(
-    atoms, lattice_constants, n_replications_x, n_replications_y)
-
-# Escreva o arquivo .xyz com a estrutura replicada
-OUTPUT_STRUCTURE_FILE = 'src/simulations/structure.xyz'
+    # Escreva o arquivo .xyz com a estrutura replicada
+    OUTPUT_STRUCTURE_FILE = 'src/simulations/pristine_structure.xyz'
 
-write_xyz(OUTPUT_STRUCTURE_FILE, n_replications_x *
-          n_replications_y * n_atoms, comment, replicated_atoms)
+    write_xyz(OUTPUT_STRUCTURE_FILE, n_replications_x *
+            n_replications_y * n_atoms, comment, replicated_atoms)
 
-print('Estrutura replicada com sucesso! arquivo salvo em {}'.format(
-    OUTPUT_STRUCTURE_FILE))
+    print('Estrutura "pristine" replicada com sucesso! arquivo salvo em {}'.format(
+        OUTPUT_STRUCTURE_FILE))