def Task4b_iv_avg():
print("TASK : Task4b_iv_avg")
maxTime = 0.7
t, N, T = SetTime(maxTime, increments)
vac = []
sampling = 5
for i in range(0, sampling):
particles = MDGenerators.PopulateCreateCrystalStructure(
4, "Ar", 1.7, N, constants.mass, 190)
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime,
N)
vag, diffu_coeff = MDFunctions.ComputeVelocityAutoCorrelation(
t, particles)
vac.append(vag)
avgVag = vac[0]
for i in range(0, sampling):
avgVag += vac[i]
avgVag[0] /= sampling
chartName = f"Avg Vel AUtocorrelation {sampling}"
MDPlot.plot([avgVag], t, N, chartName, ["vac"], "time (s)", "4biv_avg")
MDFileWriter.WriteXYZFile(particles, "4b_ii", N)
MDFileWriter.WriteLastFrame(particles, "4b_iiii_lastFrame", N)
def Task3d_ii():
print("TASK : Task3d_i")
maxTime = 5 #should be 3
t, N, T = SetTime(maxTime, increments)
nthFrame = 10
dist = 1.7
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('left', 'Ar', np.array([0., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([dist, 0.0, 0.0]), v0, N,
constants.mass)
]
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDFunctions.MoveToCentreOfBox(particles)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Velocity Verlet) 1.5 sigma",
"3dii_energy_two")
MDFileWriter.WriteXYZFile(particles, "3dii_two", N)
particles = MDGenerators.PopulateCreateCrystalStructure(
1, "AR", dist, N, constants.mass)
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDPlot.plotAllEnergies(
particles, t, "Total Energy (Velocity Verlet) 4 particles, random",
"3dii_energy_four")
MDFileWriter.WriteXYZFile(particles, "3dii_four", N, nthFrame)
def Task2FasterCompare2():
print("TASK : Task2FasterCompare2")
maxTime = 0.7
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([1.5, 0.0, 0.0]), v0, N,
constants.mass)
]
#particles = [MDParticle.Particle('left', 'Ar', np.array([0.0,0.0,0.0] ), v0, N, constants.mass)]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solve(MDSolver.velocityVerlet, particles, T, N)
#MDSolver.solve(MDSolver.eulerCromer, particles, T, N)
MDPlot.plotAllEnergies(particles, t, "Test slow", "testSlow")
MDFileWriter.WriteXYZFile(particles, "twoparticlesVelVerSlow", N, 50)
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([1.5, 0.0, 0.0]), v0, N,
constants.mass)
]
#particles = [MDParticle.Particle('left', 'Ar', np.array([0.0,0.0,0.0] ), v0, N, constants.mass)]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, T, N)
MDPlot.plotAllEnergies(particles, t, "Test fast", "testFast")
MDFileWriter.WriteXYZFile(particles, "twoparticlesVelVerFast", N, 50)
def Task3b_ii():
print("TASK : Task3b_ii")
maxTime = 5
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
print("Simulating four atom")
## Create particless
particles = [
MDParticle.Particle('one', 'Ar', np.array([1., 0.0, 0.]), v0, N,
constants.mass),
MDParticle.Particle('two', 'Ar', np.array([0., 1., 0.]), v0, N,
constants.mass),
MDParticle.Particle('three', 'Ar', np.array([-1., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('four', 'Ar', np.array([0., -1., 0.]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Velocity Verlet)(fast) 1.0 sigma",
"allEnergies15velocityVerlet15fast")
MDFileWriter.WriteXYZFile(particles, "fourparticlesVelVer1Fast", N)
def Task2c_i():
print("TASK : Task2c_i")
maxTime = 5
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([1.5, 0.0, 0.0]), v0, N,
constants.mass)
]
MDSolver.solve(MDSolver.eulerCromer, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Euler Cromer) 1.5 sigma",
"2ci_allEnergiesCromer095")
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([0.95, 0.0, 0.0]), v0, N,
constants.mass)
]
MDSolver.solve(MDSolver.eulerCromer, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Euler Cromer) 0.95 sigma",
"2ci_allEnergiesCromer15")
def Task3a_iiii():
print("TASK : Task3a_iiii")
print("Verify the shifted potential")
MDPlot.plotPotential(0.9, 5, "Plot potential (shifted and unmodified)",
"plotPotential")
MDPlot.plotShiftedPotentialDiff(0.90, 5,
"Plot potential (shifted and unmodified)",
"plotPotentialDiff")
def Task3d_i():
print("TASK : Task3d_i")
maxTime = 3 #should be 3
t, N, T = SetTime(maxTime, increments)
nthFrame = 10
particles = MDGenerators.PopulateCreateCrystalStructure(
4, "AR", 1.7, N, constants.mass)
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDPlot.plotAllEnergies(
particles, t, "Total Energy (Velocity Verlet) 256 particles, random",
"3d_ii")
MDFileWriter.WriteXYZFile(particles, "256_random", N, nthFrame)
def Task4a_iii_fast():
print("TASK : Task4a_iii")
maxTime = 10
t, N, T = SetTime(maxTime, increments)
t_initial = 190
particles = MDGenerators.PopulateCreateCrystalStructure(
3, "Ar", 1.7, N, constants.mass, t_initial)
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
#temp = MDFunctions.ComputeTemperatureReduced(N-1, particles, constants.eps)
#print(f"AT time {maxTime} temperature is {temp} kelvin")
chartName = f"4a) iii Temp ({t_initial} K) (fast)"
MDPlot.plotTemperature(particles, t, N, chartName, "4a_iii_fast")
def Task4a_ii_fast():
print("TASK : Task4a_ii")
maxTime = 1.5
t, N, T = SetTime(maxTime, increments)
t_initial = 300
particles = MDGenerators.PopulateCreateCrystalStructure(
3, "Ar", 1.7, N, constants.mass, t_initial)
MDFileWriter.WriteFirstFrame(particles, "firstFrame", N)
#MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
#MDSolver.solve(MDSolver.velocityVerlet, particles, maxTime, N, constants.eps, constants.sig)
MDFileWriter.WriteXYZFile(particles, "checkthis_fast", N)
chartName = f"4a) ii Temp ({t_initial} K) (fast)"
MDPlot.plotTemperature(particles, t, N, chartName, "4a_ii_fast")
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 Task2b_iv():
print("TASK : Task2b_iv")
maxTime = 5
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([0.95, 0.0, 0.0]), v0, N,
constants.mass)
]
MDSolver.solve(MDSolver.eulerCromer, particles, T, N)
MDPlot.plotDistanceBetween(t, "Distance, sig = 0.95", particles[0],
particles[1], "two-particle-distance-095")
def Task4c_ii():
print("TASK : Task4c_ii")
maxTime = 0.7
t, N, T = SetTime(maxTime, increments)
particles = MDGenerators.PopulateCreateCrystalStructure(
6, "Ar", 1.7, N, constants.mass, 190)
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDPlot.plotMeanSquaredDisplacement(particles, t, N, constants.eps,
"4c) i - Mean squared displacement",
True, "4c_ii")
MDFileWriter.WriteXYZFile(particles, "4c_ii", N)
MDFileWriter.WriteLastFrame(particles, "4c_ii_lastFrame", N)
def Task4b_v():
print("TASK : Task4b_v")
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)
MDPlot.plotVelocityAutoCorrelation(particles, t, N,
"4b) ii - Vel.Corr / Diff.coeff ",
"4b_v")
MDFileWriter.WriteXYZFile(particles, "4b_v", N)
MDFileWriter.WriteLastFrame(particles, "4b_v_lastFrame", N)
def Task4b_iii():
print("TASK : Task4b_iii")
beginTime = 0.7
maxTime = 1.5
t, N, T = SetTime(maxTime, increments, beginTime)
particles = MDFileWriter.ReadInitialConditions("4b_ii_lastFrame", N,
constants.mass)
#MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDPlot.plotVelocityAutoCorrelation(
particles, t, N, "4b) iii - Velocity autocorrelation plot", "4b_iii")
MDFileWriter.WriteXYZFile(particles, "4b_iii", N)
MDFileWriter.WriteLastFrame(particles, "4b_iii_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}")
def Task3b_iv():
print("TASK : Task3b_iv")
maxTime = 5
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('one', 'Ar', np.array([1., 0.0, 0.]), v0, N,
constants.mass),
MDParticle.Particle('two', 'Ar', np.array([0., 1., 0.]), v0, N,
constants.mass),
MDParticle.Particle('three', 'Ar', np.array([-1., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('four', 'Ar', np.array([0., -1., 0.]), v0, N,
constants.mass)
]
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Velocity Verlet) 4 particles",
"3b_iv")
MDFileWriter.WriteXYZFile3(particles, "3b_iv", N)
def Task3b_v():
print("TASK : Task3b_v")
print("Simulating four atom")
nthFrame = 10
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('one', 'Ar', np.array([1., 0.1, 0.]), v0, N,
constants.mass),
MDParticle.Particle('two', 'Ar', np.array([0., 1., 0.]), v0, N,
constants.mass),
MDParticle.Particle('three', 'Ar', np.array([-1., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('four', 'Ar', np.array([0., -1., 0.]), v0, N,
constants.mass)
]
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, T, N)
MDPlot.plotAllEnergies(
particles, t, "Total Energy (Velocity Verlet) 4 particles, perturbed",
"3b_v")
MDFileWriter.WriteXYZFile(particles, "fourparticlesVelVer1FastPerturb", N,
nthFrame)
def Task2c_iv():
print("TASK : Task2c_iv")
maxTime = 5
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
particles = [
MDParticle.Particle('left', 'Ar', np.array([0., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([1.5, 0.0, 0.0]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solve(MDSolver.euler, particles, T, N)
MDPlot.plotAllEnergies(particles, t, "Total Energy (Euler) 1.5 sigma",
"2civ_allEnergiesEuler15")
MDFileWriter.WriteXYZFile(particles, "twoparticlesEuler15", N)
particles = [
MDParticle.Particle('left', 'Ar', np.array([0., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([1.5, 0.0, 0.0]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solve(MDSolver.eulerCromer, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Euler Cromer) 1.5 sigma",
"2civ_allEnergiesEulerCromer15")
MDFileWriter.WriteXYZFile(particles, "twoparticlesEulerCromer15", N)
particles = [
MDParticle.Particle('left', 'Ar', np.array([0., 0., 0.]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([1.5, 0.0, 0.0]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solve(MDSolver.velocityVerlet, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Velocity Verlet) 1.5 sigma",
"2civ_allEnergiesVelocityVerlet15")
MDFileWriter.WriteXYZFile(particles, "twoparticlesVelVer15", N)
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([0.95, 0.0, 0.0]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solve(MDSolver.eulerCromer, particles, T, N)
MDPlot.plotAllEnergies(particles, t, "Total Energy (Euler) 0.95 sigma",
"2civ_allEnergiesEuler095")
MDFileWriter.WriteXYZFile(particles, "twoparticlesEuler095", N)
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([0.95, 0.0, 0.0]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDFileWriter.WriteXYZFile(particles, "twoparticlesEulerCromer095", N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Euler Cromer) 0.95 sigma",
"2civ_allEnergiesEulerCromer095")
MDFileWriter.WriteXYZFile(particles, "twoparticlesEulerCromer095", N)
particles = [
MDParticle.Particle('left', 'Ar', np.array([0.0, 0.0, 0.0]), v0, N,
constants.mass),
MDParticle.Particle('right', 'Ar', np.array([0.95, 0.0, 0.0]), v0, N,
constants.mass)
]
MDFunctions.MoveToCentreOfBox(particles)
MDSolver.solve(MDSolver.velocityVerlet, particles, T, N)
MDPlot.plotAllEnergies(particles, t,
"Total Energy (Velocity Verlet) 0.95 sigma",
"2civ_allEnergiesVelocityVerlet095")
MDFileWriter.WriteXYZFile(particles, "twoparticlesVelVer095", N)