def startMeasurement(filepath, file_type, covalent_radii_cut_off, c, n1, n2,
calculate):
if n1 > n2:
print("Final m cannot be smaller than initial m")
return
print("Starting script...")
slab = read(filepath)
total_particles = len(slab)
print("Slab %s read with success. Total particles %d" %
(filepath, total_particles))
print("Creating graph...")
if file_type == 'V':
G = generateGraphFromSlabVinkFile(slab, covalent_radii_cut_off)
else:
G = generateGraphFromSlab(slab, covalent_radii_cut_off)
total_nodes = G.get_total_nodes()
if total_nodes == 0 or G.get_total_edges() == 0:
print("No edges found in graph. Check covalent_radii_cut_off")
return
print("Graph created with success. Nodes found: %d" % total_nodes)
cell = slab.get_cell()
# somente para celulas ortogonais
if not is_orthorhombic(cell):
print("Unit cell is not orthorhombic")
return
measurement = Measurement()
measurement.fromFile(filepath, covalent_radii_cut_off, c, n1, n2)
measurement.createFile()
(pbcX, pbcY, pbcZ) = slab.get_pbc()
(dmin, dmax) = getMaxMinSlabArray(slab)
maxM = getNumberRandomPositions(n2 - 1, total_particles)
configurationalEntropy = bg.ConfigurationalEntropy(G, 3, len(slab), pbcX,
pbcY, pbcZ, maxM)
configurationalEntropy.add_positions(slab.get_positions(wrap=True))
print("Generating random positions...")
configurationalEntropy.init_search(0, cell[0][0], 0, cell[1][1], 0,
cell[2][2], n2 - 1, maxM, dmin, dmax)
print("Random positions generated.")
H_n_values = []
for n in range(n1, n2):
measurement.start()
m = getNumberRandomPositions(n, total_particles)
H_n, H1n = run(configurationalEntropy, m, n, c)
measurement.writeResult(n, m, H_n, H1n)
measurement.end()
H_n_values.append((n, H_n, H1n, "Y"))
calculateConfigurationalEntropy(n1, n2, H_n_values, c, calculate)
print("Program ended correctly")
