def Task3b_i():
print("TASK : Task3b_i")
maxTime = 5
t, N, T = SetTime(maxTime, increments)
v0 = np.array([0, 0, 0])
print("Verification by reproduction of the two atom simulation")
## Create particless
#createParticles(3, "AR", 1, particles, T, N)
# solveFaster(velocityVerletFast2, particles, T, N, constants.cutOffRange)
#WriteXYZFile(particles,"threeparticlesVelFast")
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)
]
MDSolver.solve(MDSolver.velocityVerlet, particles, T, N)
#MDPlot.plotAllEnergies(particles, t, "Total Energy (Velocity Verlet) 1.5 sigma", "allEnergies15velocityVerlet15")
MDFileWriter.WriteXYZFile(particles, "twoparticlesVelVer15", 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)
]
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, T, N)
#MDPlot.plotAllEnergies(particles, t, "Total Energy (Velocity Verlet)(fast) 1.5 sigma", "allEnergies15velocityVerlet15fast")
MDFileWriter.WriteXYZFile(particles, "twoparticlesVelVer15Fast", N)
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 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 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 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 Task3c_i():
print("TASK : Task3c_i")
maxTime = 3 #should be 3
t, N, T = SetTime(maxTime, increments)
nthFrame = 10
particles = MDGenerators.PopulateCreateCrystalStructure(
3, "AR", 1, N, constants.mass)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDFileWriter.WriteXYZFile(particles, "crystal", N, nthFrame)
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 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 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 Task3e_ii():
print("TASK : Task3e_ii")
maxTime = 1 #should be 3
nthFrame = 1
t, N, T = SetTime(maxTime, increments)
particles = MDGenerators.PopulateCreateCrystalStructure(
2, "AR", 1.7, N, constants.mass)
MDFunctions.MoveToCentreOfBox(particles)
#MDFileWriter.WriteXYZFile(particles, "108_initial", N, nthFrame)
#MDSolver.solve(MDSolver.velocityVerlet, particles, T, N)
MDSolver.solveFaster(MDSolver.velocityVerletFast2, particles, maxTime, N)
MDFileWriter.WriteXYZFile(particles, "108_initial", N, nthFrame)
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 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)