def Task4b_ii():
print("TASK : Task4b_ii")
maxTime = 0.7
t, N, T = SetTime(maxTime, increments)
#particles = MDGenerators.PopulateCreateCrystalStructure(4, "Ar", 1.7, N, constants.mass, 190)
#MDFunctions.MoveToCentreOfBox(particles)
#MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
particles = MDFileWriter.ReadEverything("4b_ii_everything", N)
MDPlot.plotVelocityAutoCorrelation(particles, t, N, "4b) ii", True,
"4b_ii")
MDFileWriter.WriteXYZFile(particles, "4b_ii", N)
MDFileWriter.WriteLastFrame(particles, "4b_ii_lastFrame", N)
def Task4_di_read(t, filename):
num_bins = 10
bin_edges = np.linspace(0, 5, num_bins + 1)
bin_centres = 0.5 * (bin_edges[1:] + bin_edges[:-1])
V = constants.box**3
#Read the file prepared by the previous
particles, maxTindex = MDFileWriter.ReadEverything(filename, N)
#Convert x-axis units from sigma to Ångstrøm
bin_centres = MDFunctions.SigmaToAngstrom(bin_centres)
if t is None:
t = maxTindex
elif t > maxTindex:
raise Exception(
"Trying to read out rdf from frame {t} which only simulated {maxTindex} frames"
)
tInSeconds = MDFunctions.ArgonTimeToSeconds(t)
count = len(particles)
x = np.array([[0., 0., 0.] for i in range(count)]) # Velocity
j = 0
counter = 0
for j in range(0, count):
x[counter] = particles[j].x[t]
counter += 1
#x = np.where(x > 0)
#Bin the distance counts
data = MDFunctions.rdf(bin_edges, x, V)
chartName = f"Ar N={count} RDF after {tInSeconds[0]:11.6} {tInSeconds[1]}"
# def barchart(data, xlabels, chartName, filename = "barChart"):
MDPlot.barchart(data, bin_centres, "RDF", chartName, f"RDF_{filename}")
strLabels = []
for lb in bin_centres[0]:
strLabels.append(f"{lb:11.1f}")