Note
Go to the end to download the full example code.
Molecular dynamics#
Note
These examples can be run without asap3 installed. In that case,
ASE’s Python implementation of the EMT calculator can be used instead, but it
is much slower.
Goal#
In this tutorial, we will learn how to perform basic molecular dynamics (MD) simulations using ASE.
The key objectives are:
Understand how to set up a crystal structure (Cu atoms on an FCC lattice).
Initialize velocities from Maxwell–Boltzmann distribution corresponding to a chosen temperature.
Integrate Newton’s equations of motion using Velocity-Verlet algorithm and we monitor the temperature using Langevin thermostat.
Monitor and analyze thermodynamic quantities (potential energy, kinetic energy, total energy, temperature).
Save trajectories and visualize atomic motion with ASE’s GUI.
Explore MD in different scenarios: - Constant energy MD (NVE ensemble) - Constant temperature MD (NVT ensemble) - Isolated nanoparticle simulations
By the end of this tutorial, you should be able to set up your own MD simulations, monitor energy conservation, and visualize system evolution.
Part 1: Basic Molecular Dynamics Simulation#
We start by creating a copper crystal, assigning random velocities corresponding to Maxwell Boltzmann Distribution at 300 K, and running dynamics in the NVE ensemble (constant energy).
import matplotlib.pyplot as plt
import numpy as np
# choose one of the following implementations of EMT:
# included in ase
# from ase.calculators.emt import EMT
# faster performance
from asap3 import EMT
from ase import units
from ase.cluster.cubic import FaceCenteredCubic as ClusterFCC
from ase.io.trajectory import Trajectory
from ase.lattice.cubic import FaceCenteredCubic as LatticeFCC
from ase.md.langevin import Langevin # for later NPT simulations
from ase.md.velocitydistribution import (
MaxwellBoltzmannDistribution,
Stationary,
ZeroRotation,
)
from ase.md.verlet import VelocityVerlet
from ase.optimize import QuasiNewton
from ase.visualize.plot import plot_atoms
# Set up initial positions of Cu atoms on Fcc crystal lattice
size = 10
atoms = LatticeFCC(
directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Cu',
size=(size, size, size),
pbc=True,
)
Before setting up the MD simulation, we take a look at the initial structure:
fig, ax = plt.subplots(figsize=(5, 5))
plot_atoms(atoms, ax, rotation=('45x,45y,0z'), show_unit_cell=2, radii=0.75)
ax.set_axis_off()
plt.tight_layout()
plt.show()
Now let’s run the MD simulation and monitor the kinetic and potential energy of the whole system:
# Describe the interatomic interactions with the Effective Medium Theory (EMT)
atoms.calc = EMT()
# Set the initial velocities corresponding to T=300K from Maxwell Boltzmann
# Distribution
MaxwellBoltzmannDistribution(atoms, temperature_K=300)
# We use Velocity Verlet algorithm to integrate the Newton's equations.
timestep_fs = 5
dyn = VelocityVerlet(atoms, timestep_fs * units.fs) # 5 fs time step.
def printenergy(a):
"""
Function to print the thermodynamical properties i.e potential energy,
kinetic energy and total energy
"""
epot = a.get_potential_energy()
ekin = a.get_kinetic_energy()
temp = a.get_temperature()
print(
f'Energy per atom: Epot ={epot:6.3f}eV Ekin = {ekin:.3f}eV '
f'(T={temp:.3f}K) Etot = {epot + ekin:.3f}eV'
)
# Now run the dynamics
print('running a NVE simulation of fcc Cu')
printenergy(atoms)
# init lists to for energy vs time data
time_ps, epot, ekin = [], [], []
mdind = 0
steps_per_block = 10
for i in range(20):
dyn.run(steps_per_block)
mdind += steps_per_block
printenergy(atoms)
# save the energies of the current MD step
time_ps.append(mdind * timestep_fs / 1000.0)
epot.append(atoms.get_potential_energy())
ekin.append(atoms.get_kinetic_energy())
etot = np.array(epot) + np.array(ekin)
# Plot energies vs time
fig, ax = plt.subplots(figsize=(6, 4))
ax.plot(time_ps, epot, label='Potential energy')
ax.plot(time_ps, ekin, label='Kinetic energy')
ax.plot(time_ps, etot, label='Total energy')
ax.set_xlabel('Time (ps)')
ax.set_ylabel('Energy (eV)')
ax.legend(loc='best')
ax.grid(True, linewidth=0.5, alpha=0.5)
plt.tight_layout()
plt.show()
/builds/ase/ase-deploy/examples/tutorials/md.py:98: DeprecationWarning: Use thermalize_momenta
MaxwellBoltzmannDistribution(atoms, temperature_K=300)
running a NVE simulation of fcc Cu
Energy per atom: Epot =-2.405eV Ekin = 156.126eV (T=301.961K) Etot = 153.721eV
Energy per atom: Epot =118.407eV Ekin = 36.103eV (T=69.826K) Etot = 154.510eV
Energy per atom: Epot =79.044eV Ekin = 75.324eV (T=145.683K) Etot = 154.368eV
Energy per atom: Epot =70.548eV Ekin = 83.668eV (T=161.821K) Etot = 154.216eV
Energy per atom: Epot =70.356eV Ekin = 83.817eV (T=162.109K) Etot = 154.173eV
Energy per atom: Epot =81.205eV Ekin = 73.131eV (T=141.442K) Etot = 154.336eV
Energy per atom: Epot =78.098eV Ekin = 76.223eV (T=147.422K) Etot = 154.321eV
Energy per atom: Epot =74.347eV Ekin = 79.886eV (T=154.507K) Etot = 154.233eV
Energy per atom: Epot =73.592eV Ekin = 80.650eV (T=155.984K) Etot = 154.242eV
Energy per atom: Epot =78.919eV Ekin = 75.393eV (T=145.818K) Etot = 154.313eV
Energy per atom: Epot =75.577eV Ekin = 78.696eV (T=152.204K) Etot = 154.272eV
Energy per atom: Epot =75.241eV Ekin = 79.016eV (T=152.823K) Etot = 154.257eV
Energy per atom: Epot =77.273eV Ekin = 77.005eV (T=148.935K) Etot = 154.279eV
Energy per atom: Epot =76.742eV Ekin = 77.535eV (T=149.959K) Etot = 154.277eV
Energy per atom: Epot =75.471eV Ekin = 78.796eV (T=152.398K) Etot = 154.267eV
Energy per atom: Epot =75.145eV Ekin = 79.131eV (T=153.046K) Etot = 154.276eV
Energy per atom: Epot =75.727eV Ekin = 78.541eV (T=151.905K) Etot = 154.268eV
Energy per atom: Epot =78.367eV Ekin = 75.905eV (T=146.808K) Etot = 154.273eV
Energy per atom: Epot =74.751eV Ekin = 79.521eV (T=153.801K) Etot = 154.272eV
Energy per atom: Epot =75.238eV Ekin = 79.027eV (T=152.845K) Etot = 154.265eV
Energy per atom: Epot =79.249eV Ekin = 75.039eV (T=145.131K) Etot = 154.288eV
Note how the total energy is conserved, but the kinetic energy quickly drops to half the expected value. Why?
What you learned here:
How to set up a basic MD run.
How to monitor the energy over time.
That total energy is approximately conserved in NVE simulations, what is the error in total energy?
Exercise: Tune the time step from 5fs to 10fs and 50fs, what changes do you observe in total energy?
Part 2: Constant temperature MD#
In many cases, you want to control temperature (NVT ensemble). This
can be done using a thermostat, like – in this tutorial – Langevin
thermostat.
Compared to the previous example, we replace the line
dyn = VelocityVerlet(...) with
where T is the desired temperature in Kelvin. For that we also imported
the Langevin in the beginning.
The Langevin dynamics will then slowly adjust the total energy of the system so the temperature approaches the desired one.
As a slightly less boring example, let us use this to melt a chunk of
copper by starting the simulation without any momentum of the atoms
(no kinetic energy), and with a desired temperature above the melting
point. We will also save information about the atoms in a trajectory
file called moldyn3.traj.
Note
It is recommended to use the asap3 implementation of the EMT
calculator here, because its performance benefits over the ase
implementation.
size = 10
T = 1500 # Kelvin
# Set up a crystal
atoms = LatticeFCC(
directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Cu',
size=(size, size, size),
pbc=False,
)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.calc = EMT()
# We want to run MD with constant energy using the Langevin algorithm
# with a time step of 5 fs, the temperature T and the friction
# coefficient to 0.02 atomic units.
timestep_fs = 5
dyn = Langevin(
atoms, timestep=timestep_fs * units.fs, temperature_K=T, friction=0.02
)
# We also want to save the positions of all atoms after every 100th time step.
traj = Trajectory('fccCu_NPT.traj', 'w', atoms)
# Now run the dynamics
print('running a NVT simulation of fcc Cu')
printenergy(atoms)
time_ps, temperature = [], []
mdind = 0
steps_per_block = 10
for i in range(200):
dyn.run(steps_per_block)
mdind += steps_per_block
printenergy(atoms)
# save the temperature of the current MD step
time_ps.append(mdind * timestep_fs / 1000.0)
temperature.append(atoms.get_temperature())
# Plot temperatures vs time
fig, ax = plt.subplots(figsize=(6, 4))
ax.plot(time_ps, temperature)
ax.set_xlabel('Time (ps)')
ax.set_ylabel('Temperature (K)')
ax.grid(True, linewidth=0.5, alpha=0.5)
plt.tight_layout()
plt.show()
/home/ase/.local/lib/python3.13/site-packages/ase/md/langevin.py:110: FutureWarning: The implementation of `fixcm=True` in `Langevin` does not strictly sample the correct NVT distributions. The deviations are typically small for large systems but can be more pronounced for small systems. Use `fixcm=False` together with `ase.constraints.FixCom`. `fixcm` is deprecated since ASE 3.28.0 and will be removed in a future release.
warnings.warn(msg, FutureWarning)
running a NVT simulation of fcc Cu
Energy per atom: Epot =540.816eV Ekin = 0.000eV (T=0.000K) Etot = 540.816eV
Energy per atom: Epot =599.754eV Ekin = 82.742eV (T=160.030K) Etot = 682.496eV
Energy per atom: Epot =671.452eV Ekin = 143.857eV (T=278.233K) Etot = 815.309eV
Energy per atom: Epot =730.469eV Ekin = 200.447eV (T=387.683K) Etot = 930.916eV
Energy per atom: Epot =781.088eV Ekin = 255.236eV (T=493.648K) Etot = 1036.324eV
Energy per atom: Epot =838.324eV Ekin = 295.353eV (T=571.239K) Etot = 1133.677eV
Energy per atom: Epot =881.236eV Ekin = 342.765eV (T=662.938K) Etot = 1224.001eV
Energy per atom: Epot =924.081eV Ekin = 379.342eV (T=733.680K) Etot = 1303.423eV
Energy per atom: Epot =961.014eV Ekin = 413.044eV (T=798.863K) Etot = 1374.058eV
Energy per atom: Epot =1004.408eV Ekin = 440.253eV (T=851.488K) Etot = 1444.661eV
Energy per atom: Epot =1044.856eV Ekin = 463.410eV (T=896.275K) Etot = 1508.265eV
Energy per atom: Epot =1088.001eV Ekin = 485.107eV (T=938.240K) Etot = 1573.108eV
Energy per atom: Epot =1105.887eV Ekin = 519.608eV (T=1004.968K) Etot = 1625.496eV
Energy per atom: Epot =1138.143eV Ekin = 537.651eV (T=1039.864K) Etot = 1675.794eV
Energy per atom: Epot =1188.944eV Ekin = 535.709eV (T=1036.107K) Etot = 1724.652eV
Energy per atom: Epot =1199.943eV Ekin = 564.435eV (T=1091.666K) Etot = 1764.378eV
Energy per atom: Epot =1236.109eV Ekin = 574.412eV (T=1110.963K) Etot = 1810.521eV
Energy per atom: Epot =1261.621eV Ekin = 577.572eV (T=1117.074K) Etot = 1839.192eV
Energy per atom: Epot =1284.743eV Ekin = 591.687eV (T=1144.374K) Etot = 1876.430eV
Energy per atom: Epot =1313.336eV Ekin = 591.944eV (T=1144.870K) Etot = 1905.280eV
Energy per atom: Epot =1333.165eV Ekin = 618.898eV (T=1197.002K) Etot = 1952.063eV
Energy per atom: Epot =1356.785eV Ekin = 622.708eV (T=1204.372K) Etot = 1979.493eV
Energy per atom: Epot =1371.087eV Ekin = 640.002eV (T=1237.819K) Etot = 2011.088eV
Energy per atom: Epot =1385.363eV Ekin = 653.582eV (T=1264.085K) Etot = 2038.946eV
Energy per atom: Epot =1422.383eV Ekin = 644.453eV (T=1246.428K) Etot = 2066.835eV
Energy per atom: Epot =1422.918eV Ekin = 672.125eV (T=1299.948K) Etot = 2095.043eV
Energy per atom: Epot =1442.396eV Ekin = 673.779eV (T=1303.147K) Etot = 2116.175eV
Energy per atom: Epot =1464.540eV Ekin = 674.227eV (T=1304.014K) Etot = 2138.767eV
Energy per atom: Epot =1463.083eV Ekin = 687.994eV (T=1330.640K) Etot = 2151.077eV
Energy per atom: Epot =1489.929eV Ekin = 676.017eV (T=1307.475K) Etot = 2165.946eV
Energy per atom: Epot =1509.019eV Ekin = 674.086eV (T=1303.742K) Etot = 2183.106eV
Energy per atom: Epot =1509.650eV Ekin = 698.517eV (T=1350.992K) Etot = 2208.166eV
Energy per atom: Epot =1529.498eV Ekin = 698.467eV (T=1350.897K) Etot = 2227.965eV
Energy per atom: Epot =1546.254eV Ekin = 702.362eV (T=1358.429K) Etot = 2248.616eV
Energy per atom: Epot =1548.964eV Ekin = 709.644eV (T=1372.514K) Etot = 2258.608eV
Energy per atom: Epot =1558.621eV Ekin = 714.805eV (T=1382.494K) Etot = 2273.425eV
Energy per atom: Epot =1578.194eV Ekin = 715.322eV (T=1383.495K) Etot = 2293.516eV
Energy per atom: Epot =1597.608eV Ekin = 709.364eV (T=1371.972K) Etot = 2306.973eV
Energy per atom: Epot =1609.359eV Ekin = 702.919eV (T=1359.507K) Etot = 2312.278eV
Energy per atom: Epot =1612.847eV Ekin = 717.767eV (T=1388.224K) Etot = 2330.614eV
Energy per atom: Epot =1636.976eV Ekin = 695.221eV (T=1344.618K) Etot = 2332.197eV
Energy per atom: Epot =1641.894eV Ekin = 707.953eV (T=1369.243K) Etot = 2349.847eV
Energy per atom: Epot =1639.760eV Ekin = 720.264eV (T=1393.053K) Etot = 2360.024eV
Energy per atom: Epot =1668.797eV Ekin = 704.001eV (T=1361.599K) Etot = 2372.798eV
Energy per atom: Epot =1660.298eV Ekin = 716.582eV (T=1385.932K) Etot = 2376.880eV
Energy per atom: Epot =1690.049eV Ekin = 701.966eV (T=1357.663K) Etot = 2392.015eV
Energy per atom: Epot =1684.876eV Ekin = 719.221eV (T=1391.037K) Etot = 2404.097eV
Energy per atom: Epot =1690.520eV Ekin = 730.215eV (T=1412.299K) Etot = 2420.735eV
Energy per atom: Epot =1708.517eV Ekin = 722.786eV (T=1397.932K) Etot = 2431.303eV
Energy per atom: Epot =1703.181eV Ekin = 738.323eV (T=1427.980K) Etot = 2441.503eV
Energy per atom: Epot =1718.918eV Ekin = 732.655eV (T=1417.018K) Etot = 2451.572eV
Energy per atom: Epot =1724.380eV Ekin = 743.692eV (T=1438.365K) Etot = 2468.072eV
Energy per atom: Epot =1731.705eV Ekin = 742.148eV (T=1435.379K) Etot = 2473.854eV
Energy per atom: Epot =1739.699eV Ekin = 739.366eV (T=1429.999K) Etot = 2479.065eV
Energy per atom: Epot =1748.200eV Ekin = 734.482eV (T=1420.552K) Etot = 2482.682eV
Energy per atom: Epot =1752.535eV Ekin = 749.696eV (T=1449.977K) Etot = 2502.230eV
Energy per atom: Epot =1770.595eV Ekin = 737.476eV (T=1426.343K) Etot = 2508.071eV
Energy per atom: Epot =1772.255eV Ekin = 744.415eV (T=1439.763K) Etot = 2516.670eV
Energy per atom: Epot =1785.102eV Ekin = 736.358eV (T=1424.181K) Etot = 2521.460eV
Energy per atom: Epot =1786.380eV Ekin = 746.099eV (T=1443.021K) Etot = 2532.479eV
Energy per atom: Epot =1799.871eV Ekin = 737.559eV (T=1426.503K) Etot = 2537.429eV
Energy per atom: Epot =1817.302eV Ekin = 725.480eV (T=1403.141K) Etot = 2542.782eV
Energy per atom: Epot =1805.692eV Ekin = 749.616eV (T=1449.822K) Etot = 2555.308eV
Energy per atom: Epot =1820.797eV Ekin = 744.530eV (T=1439.986K) Etot = 2565.327eV
Energy per atom: Epot =1821.269eV Ekin = 755.604eV (T=1461.404K) Etot = 2576.873eV
Energy per atom: Epot =1836.354eV Ekin = 747.757eV (T=1446.228K) Etot = 2584.111eV
Energy per atom: Epot =1836.271eV Ekin = 756.822eV (T=1463.760K) Etot = 2593.093eV
Energy per atom: Epot =1844.281eV Ekin = 745.399eV (T=1441.666K) Etot = 2589.680eV
Energy per atom: Epot =1851.597eV Ekin = 741.964eV (T=1435.022K) Etot = 2593.560eV
Energy per atom: Epot =1856.137eV Ekin = 741.594eV (T=1434.308K) Etot = 2597.731eV
Energy per atom: Epot =1864.889eV Ekin = 738.485eV (T=1428.294K) Etot = 2603.374eV
Energy per atom: Epot =1874.136eV Ekin = 740.537eV (T=1432.264K) Etot = 2614.673eV
Energy per atom: Epot =1870.532eV Ekin = 759.579eV (T=1469.091K) Etot = 2630.111eV
Energy per atom: Epot =1870.962eV Ekin = 760.562eV (T=1470.993K) Etot = 2631.524eV
Energy per atom: Epot =1859.767eV Ekin = 774.025eV (T=1497.031K) Etot = 2633.791eV
Energy per atom: Epot =1897.209eV Ekin = 751.006eV (T=1452.510K) Etot = 2648.215eV
Energy per atom: Epot =1896.348eV Ekin = 755.987eV (T=1462.145K) Etot = 2652.335eV
Energy per atom: Epot =1917.416eV Ekin = 744.895eV (T=1440.691K) Etot = 2662.311eV
Energy per atom: Epot =1915.351eV Ekin = 747.447eV (T=1445.627K) Etot = 2662.798eV
Energy per atom: Epot =1917.732eV Ekin = 747.561eV (T=1445.849K) Etot = 2665.294eV
Energy per atom: Epot =1913.658eV Ekin = 751.457eV (T=1453.384K) Etot = 2665.115eV
Energy per atom: Epot =1923.348eV Ekin = 753.468eV (T=1457.273K) Etot = 2676.816eV
Energy per atom: Epot =1916.151eV Ekin = 750.182eV (T=1450.917K) Etot = 2666.333eV
Energy per atom: Epot =1939.848eV Ekin = 734.583eV (T=1420.748K) Etot = 2674.431eV
Energy per atom: Epot =1925.528eV Ekin = 761.616eV (T=1473.031K) Etot = 2687.144eV
Energy per atom: Epot =1934.277eV Ekin = 756.386eV (T=1462.916K) Etot = 2690.663eV
Energy per atom: Epot =1931.030eV Ekin = 760.120eV (T=1470.138K) Etot = 2691.150eV
Energy per atom: Epot =1933.126eV Ekin = 762.022eV (T=1473.817K) Etot = 2695.148eV
Energy per atom: Epot =1937.033eV Ekin = 759.748eV (T=1469.420K) Etot = 2696.782eV
Energy per atom: Epot =1945.778eV Ekin = 751.258eV (T=1452.999K) Etot = 2697.037eV
Energy per atom: Epot =1950.441eV Ekin = 747.668eV (T=1446.055K) Etot = 2698.109eV
Energy per atom: Epot =1938.512eV Ekin = 772.213eV (T=1493.526K) Etot = 2710.725eV
Energy per atom: Epot =1965.780eV Ekin = 750.700eV (T=1451.920K) Etot = 2716.481eV
Energy per atom: Epot =1960.114eV Ekin = 762.827eV (T=1475.374K) Etot = 2722.941eV
Energy per atom: Epot =1954.914eV Ekin = 770.900eV (T=1490.988K) Etot = 2725.814eV
Energy per atom: Epot =1966.324eV Ekin = 760.314eV (T=1470.514K) Etot = 2726.638eV
Energy per atom: Epot =1958.850eV Ekin = 766.916eV (T=1483.282K) Etot = 2725.766eV
Energy per atom: Epot =1965.472eV Ekin = 760.164eV (T=1470.224K) Etot = 2725.636eV
Energy per atom: Epot =1967.202eV Ekin = 760.174eV (T=1470.244K) Etot = 2727.377eV
Energy per atom: Epot =1971.426eV Ekin = 760.130eV (T=1470.158K) Etot = 2731.556eV
Energy per atom: Epot =1972.655eV Ekin = 765.811eV (T=1481.145K) Etot = 2738.466eV
Energy per atom: Epot =1978.600eV Ekin = 778.168eV (T=1505.045K) Etot = 2756.768eV
Energy per atom: Epot =1994.205eV Ekin = 761.887eV (T=1473.556K) Etot = 2756.092eV
Energy per atom: Epot =1988.526eV Ekin = 765.329eV (T=1480.213K) Etot = 2753.855eV
Energy per atom: Epot =1991.088eV Ekin = 763.994eV (T=1477.630K) Etot = 2755.082eV
Energy per atom: Epot =1997.133eV Ekin = 758.842eV (T=1467.667K) Etot = 2755.976eV
Energy per atom: Epot =1992.980eV Ekin = 759.179eV (T=1468.318K) Etot = 2752.159eV
Energy per atom: Epot =1984.459eV Ekin = 772.244eV (T=1493.587K) Etot = 2756.703eV
Energy per atom: Epot =1988.634eV Ekin = 771.435eV (T=1492.023K) Etot = 2760.070eV
Energy per atom: Epot =1988.994eV Ekin = 773.573eV (T=1496.158K) Etot = 2762.567eV
Energy per atom: Epot =1990.396eV Ekin = 775.029eV (T=1498.973K) Etot = 2765.425eV
Energy per atom: Epot =2002.160eV Ekin = 762.376eV (T=1474.501K) Etot = 2764.535eV
Energy per atom: Epot =2001.715eV Ekin = 752.773eV (T=1455.928K) Etot = 2754.488eV
Energy per atom: Epot =1990.805eV Ekin = 769.247eV (T=1487.790K) Etot = 2760.052eV
Energy per atom: Epot =1984.612eV Ekin = 774.302eV (T=1497.567K) Etot = 2758.914eV
Energy per atom: Epot =1987.471eV Ekin = 768.723eV (T=1486.777K) Etot = 2756.194eV
Energy per atom: Epot =1989.553eV Ekin = 777.008eV (T=1502.800K) Etot = 2766.560eV
Energy per atom: Epot =1979.680eV Ekin = 786.285eV (T=1520.744K) Etot = 2765.966eV
Energy per atom: Epot =1996.337eV Ekin = 775.975eV (T=1500.804K) Etot = 2772.313eV
Energy per atom: Epot =1991.011eV Ekin = 776.569eV (T=1501.951K) Etot = 2767.580eV
Energy per atom: Epot =1993.833eV Ekin = 764.804eV (T=1479.198K) Etot = 2758.637eV
Energy per atom: Epot =2007.571eV Ekin = 752.283eV (T=1454.982K) Etot = 2759.854eV
Energy per atom: Epot =1999.305eV Ekin = 761.761eV (T=1473.313K) Etot = 2761.066eV
Energy per atom: Epot =2001.761eV Ekin = 762.620eV (T=1474.973K) Etot = 2764.381eV
Energy per atom: Epot =2002.524eV Ekin = 758.098eV (T=1466.228K) Etot = 2760.622eV
Energy per atom: Epot =1991.286eV Ekin = 772.939eV (T=1494.931K) Etot = 2764.225eV
Energy per atom: Epot =1996.557eV Ekin = 774.297eV (T=1497.558K) Etot = 2770.854eV
Energy per atom: Epot =1997.598eV Ekin = 777.010eV (T=1502.805K) Etot = 2774.607eV
Energy per atom: Epot =2000.468eV Ekin = 765.177eV (T=1479.920K) Etot = 2765.645eV
Energy per atom: Epot =1994.017eV Ekin = 766.359eV (T=1482.205K) Etot = 2760.376eV
Energy per atom: Epot =1987.854eV Ekin = 769.221eV (T=1487.740K) Etot = 2757.074eV
Energy per atom: Epot =1994.136eV Ekin = 761.577eV (T=1472.955K) Etot = 2755.713eV
Energy per atom: Epot =1990.736eV Ekin = 763.121eV (T=1475.943K) Etot = 2753.857eV
Energy per atom: Epot =1975.825eV Ekin = 782.022eV (T=1512.498K) Etot = 2757.847eV
Energy per atom: Epot =1991.184eV Ekin = 767.749eV (T=1484.894K) Etot = 2758.934eV
Energy per atom: Epot =1979.578eV Ekin = 770.107eV (T=1489.453K) Etot = 2749.685eV
Energy per atom: Epot =1982.827eV Ekin = 766.464eV (T=1482.409K) Etot = 2749.291eV
Energy per atom: Epot =1988.074eV Ekin = 755.151eV (T=1460.527K) Etot = 2743.225eV
Energy per atom: Epot =1992.786eV Ekin = 762.017eV (T=1473.807K) Etot = 2754.803eV
Energy per atom: Epot =1991.766eV Ekin = 773.857eV (T=1496.706K) Etot = 2765.622eV
Energy per atom: Epot =2003.972eV Ekin = 772.187eV (T=1493.476K) Etot = 2776.159eV
Energy per atom: Epot =1992.366eV Ekin = 770.510eV (T=1490.234K) Etot = 2762.877eV
Energy per atom: Epot =1998.732eV Ekin = 767.438eV (T=1484.292K) Etot = 2766.170eV
Energy per atom: Epot =1986.933eV Ekin = 780.057eV (T=1508.698K) Etot = 2766.990eV
Energy per atom: Epot =2002.781eV Ekin = 767.504eV (T=1484.420K) Etot = 2770.285eV
Energy per atom: Epot =1991.855eV Ekin = 765.215eV (T=1479.992K) Etot = 2757.070eV
Energy per atom: Epot =2007.439eV Ekin = 752.476eV (T=1455.354K) Etot = 2759.915eV
Energy per atom: Epot =2008.939eV Ekin = 765.532eV (T=1480.605K) Etot = 2774.470eV
Energy per atom: Epot =2006.910eV Ekin = 765.469eV (T=1480.484K) Etot = 2772.379eV
Energy per atom: Epot =2011.519eV Ekin = 763.443eV (T=1476.565K) Etot = 2774.961eV
Energy per atom: Epot =1999.130eV Ekin = 783.926eV (T=1516.182K) Etot = 2783.056eV
Energy per atom: Epot =2011.115eV Ekin = 768.292eV (T=1485.944K) Etot = 2779.407eV
Energy per atom: Epot =1996.151eV Ekin = 784.304eV (T=1516.913K) Etot = 2780.456eV
Energy per atom: Epot =2001.281eV Ekin = 776.330eV (T=1501.490K) Etot = 2777.611eV
Energy per atom: Epot =2010.942eV Ekin = 759.840eV (T=1469.597K) Etot = 2770.782eV
Energy per atom: Epot =2004.593eV Ekin = 763.619eV (T=1476.906K) Etot = 2768.212eV
Energy per atom: Epot =1995.955eV Ekin = 780.598eV (T=1509.745K) Etot = 2776.553eV
Energy per atom: Epot =1997.128eV Ekin = 775.280eV (T=1499.460K) Etot = 2772.408eV
Energy per atom: Epot =1996.911eV Ekin = 777.160eV (T=1503.096K) Etot = 2774.071eV
Energy per atom: Epot =1993.306eV Ekin = 779.460eV (T=1507.543K) Etot = 2772.766eV
Energy per atom: Epot =1998.821eV Ekin = 778.357eV (T=1505.410K) Etot = 2777.178eV
Energy per atom: Epot =1996.464eV Ekin = 771.308eV (T=1491.777K) Etot = 2767.772eV
Energy per atom: Epot =1993.618eV Ekin = 768.047eV (T=1485.469K) Etot = 2761.664eV
Energy per atom: Epot =1984.721eV Ekin = 776.192eV (T=1501.222K) Etot = 2760.913eV
Energy per atom: Epot =1985.678eV Ekin = 770.527eV (T=1490.267K) Etot = 2756.205eV
Energy per atom: Epot =1993.104eV Ekin = 764.625eV (T=1478.851K) Etot = 2757.729eV
Energy per atom: Epot =1977.226eV Ekin = 781.370eV (T=1511.238K) Etot = 2758.596eV
Energy per atom: Epot =1996.546eV Ekin = 767.048eV (T=1483.538K) Etot = 2763.594eV
Energy per atom: Epot =1997.166eV Ekin = 771.434eV (T=1492.021K) Etot = 2768.600eV
Energy per atom: Epot =1984.652eV Ekin = 776.454eV (T=1501.729K) Etot = 2761.106eV
Energy per atom: Epot =1999.574eV Ekin = 763.649eV (T=1476.964K) Etot = 2763.224eV
Energy per atom: Epot =1979.288eV Ekin = 775.055eV (T=1499.024K) Etot = 2754.343eV
Energy per atom: Epot =1997.591eV Ekin = 755.305eV (T=1460.826K) Etot = 2752.897eV
Energy per atom: Epot =1983.444eV Ekin = 777.573eV (T=1503.893K) Etot = 2761.016eV
Energy per atom: Epot =2007.174eV Ekin = 765.322eV (T=1480.199K) Etot = 2772.496eV
Energy per atom: Epot =1994.822eV Ekin = 768.597eV (T=1486.533K) Etot = 2763.419eV
Energy per atom: Epot =1999.811eV Ekin = 753.434eV (T=1457.207K) Etot = 2753.245eV
Energy per atom: Epot =1996.331eV Ekin = 757.089eV (T=1464.276K) Etot = 2753.420eV
Energy per atom: Epot =1991.764eV Ekin = 776.353eV (T=1501.534K) Etot = 2768.116eV
Energy per atom: Epot =2002.225eV Ekin = 761.102eV (T=1472.037K) Etot = 2763.327eV
Energy per atom: Epot =1995.922eV Ekin = 759.653eV (T=1469.234K) Etot = 2755.575eV
Energy per atom: Epot =1986.806eV Ekin = 765.888eV (T=1481.293K) Etot = 2752.694eV
Energy per atom: Epot =1997.889eV Ekin = 756.178eV (T=1462.515K) Etot = 2754.068eV
Energy per atom: Epot =1999.710eV Ekin = 760.418eV (T=1470.716K) Etot = 2760.128eV
Energy per atom: Epot =2004.154eV Ekin = 749.596eV (T=1449.783K) Etot = 2753.749eV
Energy per atom: Epot =1994.604eV Ekin = 758.760eV (T=1467.509K) Etot = 2753.364eV
Energy per atom: Epot =2001.418eV Ekin = 758.684eV (T=1467.360K) Etot = 2760.102eV
Energy per atom: Epot =1996.710eV Ekin = 763.984eV (T=1477.611K) Etot = 2760.693eV
Energy per atom: Epot =1998.669eV Ekin = 757.307eV (T=1464.698K) Etot = 2755.977eV
Energy per atom: Epot =1991.135eV Ekin = 768.045eV (T=1485.465K) Etot = 2759.179eV
Energy per atom: Epot =1988.819eV Ekin = 768.396eV (T=1486.144K) Etot = 2757.215eV
Energy per atom: Epot =1993.299eV Ekin = 767.783eV (T=1484.959K) Etot = 2761.082eV
Energy per atom: Epot =2001.516eV Ekin = 760.536eV (T=1470.942K) Etot = 2762.051eV
Energy per atom: Epot =1997.367eV Ekin = 767.590eV (T=1484.586K) Etot = 2764.957eV
Energy per atom: Epot =1997.916eV Ekin = 777.074eV (T=1502.929K) Etot = 2774.990eV
Energy per atom: Epot =1999.955eV Ekin = 769.025eV (T=1487.362K) Etot = 2768.980eV
Energy per atom: Epot =2005.440eV Ekin = 770.005eV (T=1489.258K) Etot = 2775.445eV
Energy per atom: Epot =2001.446eV Ekin = 763.125eV (T=1475.949K) Etot = 2764.570eV
Energy per atom: Epot =1996.569eV Ekin = 764.719eV (T=1479.033K) Etot = 2761.288eV
Energy per atom: Epot =1992.067eV Ekin = 771.280eV (T=1491.722K) Etot = 2763.347eV
Energy per atom: Epot =1981.490eV Ekin = 782.136eV (T=1512.719K) Etot = 2763.626eV
After running the simulation, you can study the result with the command
ase gui fccCu_NPT.traj
Try plotting the kinetic energy. Like in the temperature vs time plot you will not see a well-defined melting point due to finite size effects (including surface melting), but you will probably see an almost flat region where the inside of the system melts. The outermost layers melt at a lower temperature.
Note
The Langevin dynamics will by default keep the position and momentum of the center of mass unperturbed. This is another improvement over just setting momenta corresponding to a temperature, as we did before.
Part 3: Isolated particle MD#
When simulating isolated particles with MD, it is sometimes preferable to set random momenta corresponding to a specific temperature and let the system evolve freely. With a relatively high temperature, the is however a risk that the collection of atoms will drift out of the simulation box because the randomized momenta gave the center of mass a small but non-zero velocity too.
Let us see what happens when we propagate a nanoparticle:
size = 4
atoms = ClusterFCC(
'Cu',
surfaces=[[1, 0, 0], [1, 1, 0], [1, 1, 1]],
layers=(size, size, size),
vacuum=4,
)
# asap3 requires a non-zero cell even if pbc are not applied
atoms.cell = [40] * 3
atoms.set_pbc(False) # isolated cluster (explicit, for clarity)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.calc = EMT()
# Quick relaxation of the cluster
qn = QuasiNewton(atoms)
qn.run(fmax=0.001, steps=10)
# Set the momenta corresponding to T=1200 K
MaxwellBoltzmannDistribution(atoms, temperature_K=1200)
Stationary(atoms) # zero linear momentum
ZeroRotation(atoms) # zero angular momentum
# Run MD using the Velocity Verlet algorithm and save trajectory
dyn = VelocityVerlet(atoms, 5 * units.fs, trajectory='nanoparticleCu_NVE.traj')
print('running a NVE simulation of a Cu nanoparticle')
printenergy(atoms)
steps_per_block = 10
for i in range(200):
dyn.run(steps_per_block)
printenergy(atoms)
Step[ FC] Time Energy fmax
BFGSLineSearch: 0[ 0] 18:10:12 43.457006 1.0818
BFGSLineSearch: 1[ 1] 18:10:12 42.347659 0.2273
BFGSLineSearch: 2[ 2] 18:10:12 42.108454 0.1349
BFGSLineSearch: 3[ 3] 18:10:12 41.964817 0.1138
BFGSLineSearch: 4[ 4] 18:10:12 41.924933 0.0683
BFGSLineSearch: 5[ 5] 18:10:12 41.915346 0.0225
BFGSLineSearch: 6[ 6] 18:10:12 41.914920 0.0059
BFGSLineSearch: 7[ 7] 18:10:12 41.914872 0.0023
BFGSLineSearch: 8[ 9] 18:10:12 41.914855 0.0023
BFGSLineSearch: 9[ 10] 18:10:12 41.914851 0.0010
/builds/ase/ase-deploy/examples/tutorials/md.py:299: DeprecationWarning: Use thermalize_momenta
MaxwellBoltzmannDistribution(atoms, temperature_K=1200)
running a NVE simulation of a Cu nanoparticle
Energy per atom: Epot =41.915eV Ekin = 12.568eV (T=1045.454K) Etot = 54.482eV
Energy per atom: Epot =49.550eV Ekin = 4.974eV (T=413.748K) Etot = 54.524eV
Energy per atom: Epot =49.506eV Ekin = 5.024eV (T=417.958K) Etot = 54.530eV
Energy per atom: Epot =48.884eV Ekin = 5.642eV (T=469.379K) Etot = 54.527eV
Energy per atom: Epot =48.659eV Ekin = 5.865eV (T=487.879K) Etot = 54.524eV
Energy per atom: Epot =48.912eV Ekin = 5.612eV (T=466.871K) Etot = 54.525eV
Energy per atom: Epot =48.273eV Ekin = 6.251eV (T=519.979K) Etot = 54.524eV
Energy per atom: Epot =48.026eV Ekin = 6.499eV (T=540.654K) Etot = 54.525eV
Energy per atom: Epot =47.618eV Ekin = 6.907eV (T=574.571K) Etot = 54.525eV
Energy per atom: Epot =49.526eV Ekin = 5.005eV (T=416.345K) Etot = 54.531eV
Energy per atom: Epot =49.401eV Ekin = 5.128eV (T=426.555K) Etot = 54.529eV
Energy per atom: Epot =48.469eV Ekin = 6.054eV (T=503.590K) Etot = 54.522eV
Energy per atom: Epot =48.639eV Ekin = 5.885eV (T=489.584K) Etot = 54.524eV
Energy per atom: Epot =48.564eV Ekin = 5.958eV (T=495.649K) Etot = 54.523eV
Energy per atom: Epot =48.173eV Ekin = 6.349eV (T=528.126K) Etot = 54.522eV
Energy per atom: Epot =48.436eV Ekin = 6.087eV (T=506.346K) Etot = 54.522eV
Energy per atom: Epot =48.345eV Ekin = 6.175eV (T=513.717K) Etot = 54.520eV
Energy per atom: Epot =48.754eV Ekin = 5.768eV (T=479.846K) Etot = 54.523eV
Energy per atom: Epot =48.657eV Ekin = 5.869eV (T=488.197K) Etot = 54.525eV
Energy per atom: Epot =48.579eV Ekin = 5.946eV (T=494.640K) Etot = 54.525eV
Energy per atom: Epot =48.412eV Ekin = 6.110eV (T=508.281K) Etot = 54.522eV
Energy per atom: Epot =48.604eV Ekin = 5.922eV (T=492.661K) Etot = 54.526eV
Energy per atom: Epot =48.635eV Ekin = 5.894eV (T=490.342K) Etot = 54.529eV
Energy per atom: Epot =48.813eV Ekin = 5.714eV (T=475.338K) Etot = 54.527eV
Energy per atom: Epot =48.678eV Ekin = 5.845eV (T=486.208K) Etot = 54.522eV
Energy per atom: Epot =48.758eV Ekin = 5.764eV (T=479.514K) Etot = 54.522eV
Energy per atom: Epot =48.207eV Ekin = 6.312eV (T=525.098K) Etot = 54.519eV
Energy per atom: Epot =48.280eV Ekin = 6.243eV (T=519.353K) Etot = 54.523eV
Energy per atom: Epot =48.439eV Ekin = 6.087eV (T=506.324K) Etot = 54.526eV
Energy per atom: Epot =49.563eV Ekin = 4.967eV (T=413.153K) Etot = 54.529eV
Energy per atom: Epot =48.245eV Ekin = 6.274eV (T=521.925K) Etot = 54.519eV
Energy per atom: Epot =48.556eV Ekin = 5.969eV (T=496.563K) Etot = 54.525eV
Energy per atom: Epot =47.733eV Ekin = 6.789eV (T=564.727K) Etot = 54.522eV
Energy per atom: Epot =48.316eV Ekin = 6.208eV (T=516.439K) Etot = 54.524eV
Energy per atom: Epot =47.999eV Ekin = 6.518eV (T=542.248K) Etot = 54.518eV
Energy per atom: Epot =49.049eV Ekin = 5.478eV (T=455.728K) Etot = 54.528eV
Energy per atom: Epot =49.130eV Ekin = 5.397eV (T=448.990K) Etot = 54.527eV
Energy per atom: Epot =48.356eV Ekin = 6.164eV (T=512.779K) Etot = 54.520eV
Energy per atom: Epot =48.052eV Ekin = 6.467eV (T=537.935K) Etot = 54.519eV
Energy per atom: Epot =48.715eV Ekin = 5.806eV (T=482.980K) Etot = 54.521eV
Energy per atom: Epot =48.685eV Ekin = 5.838eV (T=485.676K) Etot = 54.524eV
Energy per atom: Epot =48.776eV Ekin = 5.748eV (T=478.161K) Etot = 54.524eV
Energy per atom: Epot =48.298eV Ekin = 6.222eV (T=517.617K) Etot = 54.520eV
Energy per atom: Epot =47.704eV Ekin = 6.814eV (T=566.868K) Etot = 54.518eV
Energy per atom: Epot =49.394eV Ekin = 5.130eV (T=426.744K) Etot = 54.524eV
Energy per atom: Epot =48.451eV Ekin = 6.071eV (T=505.020K) Etot = 54.522eV
Energy per atom: Epot =48.199eV Ekin = 6.326eV (T=526.243K) Etot = 54.525eV
Energy per atom: Epot =48.261eV Ekin = 6.264eV (T=521.076K) Etot = 54.525eV
Energy per atom: Epot =48.361eV Ekin = 6.163eV (T=512.720K) Etot = 54.524eV
Energy per atom: Epot =48.661eV Ekin = 5.864eV (T=487.782K) Etot = 54.525eV
Energy per atom: Epot =48.302eV Ekin = 6.220eV (T=517.389K) Etot = 54.521eV
Energy per atom: Epot =48.722eV Ekin = 5.808eV (T=483.114K) Etot = 54.529eV
Energy per atom: Epot =48.635eV Ekin = 5.892eV (T=490.170K) Etot = 54.527eV
Energy per atom: Epot =47.971eV Ekin = 6.551eV (T=544.922K) Etot = 54.521eV
Energy per atom: Epot =49.011eV Ekin = 5.514eV (T=458.680K) Etot = 54.525eV
Energy per atom: Epot =48.264eV Ekin = 6.259eV (T=520.669K) Etot = 54.523eV
Energy per atom: Epot =48.022eV Ekin = 6.499eV (T=540.630K) Etot = 54.521eV
Energy per atom: Epot =48.523eV Ekin = 5.998eV (T=498.994K) Etot = 54.521eV
Energy per atom: Epot =48.745eV Ekin = 5.782eV (T=480.947K) Etot = 54.527eV
Energy per atom: Epot =48.743eV Ekin = 5.784eV (T=481.134K) Etot = 54.527eV
Energy per atom: Epot =48.643eV Ekin = 5.882eV (T=489.317K) Etot = 54.525eV
Energy per atom: Epot =48.839eV Ekin = 5.681eV (T=472.581K) Etot = 54.520eV
Energy per atom: Epot =48.407eV Ekin = 6.116eV (T=508.780K) Etot = 54.523eV
Energy per atom: Epot =48.828eV Ekin = 5.697eV (T=473.883K) Etot = 54.524eV
Energy per atom: Epot =48.295eV Ekin = 6.225eV (T=517.841K) Etot = 54.521eV
Energy per atom: Epot =48.631eV Ekin = 5.890eV (T=489.953K) Etot = 54.521eV
Energy per atom: Epot =48.607eV Ekin = 5.919eV (T=492.346K) Etot = 54.526eV
Energy per atom: Epot =48.664eV Ekin = 5.861eV (T=487.539K) Etot = 54.525eV
Energy per atom: Epot =47.707eV Ekin = 6.810eV (T=566.494K) Etot = 54.517eV
Energy per atom: Epot =48.744eV Ekin = 5.783eV (T=481.067K) Etot = 54.527eV
Energy per atom: Epot =48.885eV Ekin = 5.643eV (T=469.390K) Etot = 54.528eV
Energy per atom: Epot =49.116eV Ekin = 5.412eV (T=450.224K) Etot = 54.528eV
Energy per atom: Epot =48.468eV Ekin = 6.056eV (T=503.750K) Etot = 54.524eV
Energy per atom: Epot =47.889eV Ekin = 6.631eV (T=551.595K) Etot = 54.520eV
Energy per atom: Epot =47.794eV Ekin = 6.724eV (T=559.317K) Etot = 54.518eV
Energy per atom: Epot =48.424eV Ekin = 6.099eV (T=507.389K) Etot = 54.524eV
Energy per atom: Epot =48.620eV Ekin = 5.904eV (T=491.143K) Etot = 54.524eV
Energy per atom: Epot =48.895eV Ekin = 5.633eV (T=468.574K) Etot = 54.528eV
Energy per atom: Epot =48.762eV Ekin = 5.765eV (T=479.598K) Etot = 54.527eV
Energy per atom: Epot =49.114eV Ekin = 5.413eV (T=450.281K) Etot = 54.527eV
Energy per atom: Epot =48.635eV Ekin = 5.889eV (T=489.853K) Etot = 54.523eV
Energy per atom: Epot =48.242eV Ekin = 6.278eV (T=522.266K) Etot = 54.520eV
Energy per atom: Epot =48.523eV Ekin = 5.998eV (T=498.934K) Etot = 54.521eV
Energy per atom: Epot =48.249eV Ekin = 6.272eV (T=521.753K) Etot = 54.521eV
Energy per atom: Epot =48.410eV Ekin = 6.116eV (T=508.755K) Etot = 54.525eV
Energy per atom: Epot =48.452eV Ekin = 6.075eV (T=505.322K) Etot = 54.526eV
Energy per atom: Epot =48.483eV Ekin = 6.048eV (T=503.093K) Etot = 54.530eV
Energy per atom: Epot =48.951eV Ekin = 5.578eV (T=464.038K) Etot = 54.529eV
Energy per atom: Epot =48.841eV Ekin = 5.688eV (T=473.153K) Etot = 54.529eV
Energy per atom: Epot =48.568eV Ekin = 5.960eV (T=495.799K) Etot = 54.528eV
Energy per atom: Epot =48.533eV Ekin = 5.992eV (T=498.420K) Etot = 54.525eV
Energy per atom: Epot =48.450eV Ekin = 6.074eV (T=505.306K) Etot = 54.524eV
Energy per atom: Epot =48.335eV Ekin = 6.188eV (T=514.746K) Etot = 54.523eV
Energy per atom: Epot =48.683eV Ekin = 5.839eV (T=485.763K) Etot = 54.523eV
Energy per atom: Epot =49.335eV Ekin = 5.193eV (T=431.980K) Etot = 54.528eV
Energy per atom: Epot =48.508eV Ekin = 6.015eV (T=500.406K) Etot = 54.524eV
Energy per atom: Epot =48.552eV Ekin = 5.972eV (T=496.778K) Etot = 54.524eV
Energy per atom: Epot =48.324eV Ekin = 6.194eV (T=515.297K) Etot = 54.519eV
Energy per atom: Epot =48.155eV Ekin = 6.364eV (T=529.377K) Etot = 54.519eV
Energy per atom: Epot =48.032eV Ekin = 6.489eV (T=539.795K) Etot = 54.521eV
Energy per atom: Epot =49.004eV Ekin = 5.519eV (T=459.147K) Etot = 54.524eV
Energy per atom: Epot =47.863eV Ekin = 6.653eV (T=553.424K) Etot = 54.515eV
Energy per atom: Epot =48.709eV Ekin = 5.813eV (T=483.586K) Etot = 54.522eV
Energy per atom: Epot =48.268eV Ekin = 6.256eV (T=520.446K) Etot = 54.524eV
Energy per atom: Epot =48.420eV Ekin = 6.106eV (T=507.916K) Etot = 54.526eV
Energy per atom: Epot =48.550eV Ekin = 5.970eV (T=496.646K) Etot = 54.520eV
Energy per atom: Epot =48.181eV Ekin = 6.339eV (T=527.294K) Etot = 54.520eV
Energy per atom: Epot =47.941eV Ekin = 6.581eV (T=547.478K) Etot = 54.522eV
Energy per atom: Epot =49.266eV Ekin = 5.261eV (T=437.645K) Etot = 54.527eV
Energy per atom: Epot =48.254eV Ekin = 6.266eV (T=521.224K) Etot = 54.520eV
Energy per atom: Epot =48.841eV Ekin = 5.685eV (T=472.930K) Etot = 54.526eV
Energy per atom: Epot =48.496eV Ekin = 6.030eV (T=501.589K) Etot = 54.526eV
Energy per atom: Epot =48.858eV Ekin = 5.666eV (T=471.326K) Etot = 54.524eV
Energy per atom: Epot =49.074eV Ekin = 5.452eV (T=453.497K) Etot = 54.525eV
Energy per atom: Epot =48.084eV Ekin = 6.439eV (T=535.621K) Etot = 54.523eV
Energy per atom: Epot =48.176eV Ekin = 6.342eV (T=527.602K) Etot = 54.518eV
Energy per atom: Epot =48.284eV Ekin = 6.237eV (T=518.834K) Etot = 54.521eV
Energy per atom: Epot =48.115eV Ekin = 6.409eV (T=533.116K) Etot = 54.524eV
Energy per atom: Epot =48.509eV Ekin = 6.015eV (T=500.406K) Etot = 54.525eV
Energy per atom: Epot =49.006eV Ekin = 5.521eV (T=459.272K) Etot = 54.527eV
Energy per atom: Epot =49.251eV Ekin = 5.275eV (T=438.779K) Etot = 54.526eV
Energy per atom: Epot =48.108eV Ekin = 6.412eV (T=533.403K) Etot = 54.520eV
Energy per atom: Epot =48.313eV Ekin = 6.209eV (T=516.537K) Etot = 54.523eV
Energy per atom: Epot =48.699eV Ekin = 5.824eV (T=484.461K) Etot = 54.523eV
Energy per atom: Epot =48.307eV Ekin = 6.216eV (T=517.096K) Etot = 54.523eV
Energy per atom: Epot =48.677eV Ekin = 5.844eV (T=486.152K) Etot = 54.522eV
Energy per atom: Epot =48.327eV Ekin = 6.193eV (T=515.188K) Etot = 54.520eV
Energy per atom: Epot =49.054eV Ekin = 5.473eV (T=455.244K) Etot = 54.527eV
Energy per atom: Epot =48.405eV Ekin = 6.119eV (T=508.999K) Etot = 54.524eV
Energy per atom: Epot =48.088eV Ekin = 6.434eV (T=535.216K) Etot = 54.522eV
Energy per atom: Epot =48.763eV Ekin = 5.761eV (T=479.232K) Etot = 54.524eV
Energy per atom: Epot =48.351eV Ekin = 6.175eV (T=513.639K) Etot = 54.525eV
Energy per atom: Epot =48.572eV Ekin = 5.950eV (T=494.981K) Etot = 54.522eV
Energy per atom: Epot =47.856eV Ekin = 6.664eV (T=554.324K) Etot = 54.520eV
Energy per atom: Epot =48.131eV Ekin = 6.392eV (T=531.711K) Etot = 54.523eV
Energy per atom: Epot =48.796eV Ekin = 5.728eV (T=476.478K) Etot = 54.524eV
Energy per atom: Epot =49.202eV Ekin = 5.324eV (T=442.908K) Etot = 54.526eV
Energy per atom: Epot =49.012eV Ekin = 5.514eV (T=458.658K) Etot = 54.525eV
Energy per atom: Epot =49.457eV Ekin = 5.072eV (T=421.946K) Etot = 54.529eV
Energy per atom: Epot =48.981eV Ekin = 5.548eV (T=461.499K) Etot = 54.529eV
Energy per atom: Epot =48.417eV Ekin = 6.109eV (T=508.156K) Etot = 54.525eV
Energy per atom: Epot =48.632eV Ekin = 5.892eV (T=490.119K) Etot = 54.524eV
Energy per atom: Epot =48.594eV Ekin = 5.931eV (T=493.355K) Etot = 54.525eV
Energy per atom: Epot =48.560eV Ekin = 5.965eV (T=496.205K) Etot = 54.525eV
Energy per atom: Epot =48.843eV Ekin = 5.682eV (T=472.681K) Etot = 54.525eV
Energy per atom: Epot =48.099eV Ekin = 6.421eV (T=534.140K) Etot = 54.520eV
Energy per atom: Epot =48.409eV Ekin = 6.116eV (T=508.739K) Etot = 54.525eV
Energy per atom: Epot =47.743eV Ekin = 6.777eV (T=563.753K) Etot = 54.520eV
Energy per atom: Epot =48.725eV Ekin = 5.802eV (T=482.612K) Etot = 54.527eV
Energy per atom: Epot =48.675eV Ekin = 5.847eV (T=486.370K) Etot = 54.522eV
Energy per atom: Epot =48.723eV Ekin = 5.803eV (T=482.704K) Etot = 54.526eV
Energy per atom: Epot =48.882eV Ekin = 5.645eV (T=469.602K) Etot = 54.527eV
Energy per atom: Epot =48.962eV Ekin = 5.565eV (T=462.899K) Etot = 54.527eV
Energy per atom: Epot =48.417eV Ekin = 6.106eV (T=507.918K) Etot = 54.523eV
Energy per atom: Epot =47.780eV Ekin = 6.738eV (T=560.528K) Etot = 54.518eV
Energy per atom: Epot =48.298eV Ekin = 6.229eV (T=518.137K) Etot = 54.527eV
Energy per atom: Epot =48.501eV Ekin = 6.028eV (T=501.424K) Etot = 54.529eV
Energy per atom: Epot =49.025eV Ekin = 5.504eV (T=457.822K) Etot = 54.528eV
Energy per atom: Epot =48.770eV Ekin = 5.755eV (T=478.726K) Etot = 54.525eV
Energy per atom: Epot =48.857eV Ekin = 5.669eV (T=471.572K) Etot = 54.526eV
Energy per atom: Epot =48.716eV Ekin = 5.810eV (T=483.281K) Etot = 54.526eV
Energy per atom: Epot =48.212eV Ekin = 6.308eV (T=524.747K) Etot = 54.520eV
Energy per atom: Epot =48.074eV Ekin = 6.445eV (T=536.144K) Etot = 54.519eV
Energy per atom: Epot =48.312eV Ekin = 6.214eV (T=516.894K) Etot = 54.526eV
Energy per atom: Epot =47.996eV Ekin = 6.531eV (T=543.267K) Etot = 54.527eV
Energy per atom: Epot =48.952eV Ekin = 5.575eV (T=463.726K) Etot = 54.527eV
Energy per atom: Epot =47.551eV Ekin = 6.966eV (T=579.466K) Etot = 54.517eV
Energy per atom: Epot =48.264eV Ekin = 6.263eV (T=521.006K) Etot = 54.527eV
Energy per atom: Epot =48.975eV Ekin = 5.553eV (T=461.972K) Etot = 54.529eV
Energy per atom: Epot =48.526eV Ekin = 5.996eV (T=498.813K) Etot = 54.522eV
Energy per atom: Epot =47.868eV Ekin = 6.650eV (T=553.158K) Etot = 54.518eV
Energy per atom: Epot =48.446eV Ekin = 6.074eV (T=505.285K) Etot = 54.520eV
Energy per atom: Epot =48.627eV Ekin = 5.900eV (T=490.817K) Etot = 54.527eV
Energy per atom: Epot =48.555eV Ekin = 5.973eV (T=496.875K) Etot = 54.528eV
Energy per atom: Epot =49.156eV Ekin = 5.370eV (T=446.687K) Etot = 54.526eV
Energy per atom: Epot =48.493eV Ekin = 6.028eV (T=501.430K) Etot = 54.521eV
Energy per atom: Epot =48.300eV Ekin = 6.221eV (T=517.544K) Etot = 54.522eV
Energy per atom: Epot =48.957eV Ekin = 5.566eV (T=463.038K) Etot = 54.523eV
Energy per atom: Epot =48.585eV Ekin = 5.938eV (T=493.976K) Etot = 54.523eV
Energy per atom: Epot =48.405eV Ekin = 6.120eV (T=509.076K) Etot = 54.524eV
Energy per atom: Epot =48.894eV Ekin = 5.635eV (T=468.761K) Etot = 54.529eV
Energy per atom: Epot =48.826eV Ekin = 5.704eV (T=474.513K) Etot = 54.531eV
Energy per atom: Epot =48.761eV Ekin = 5.765eV (T=479.566K) Etot = 54.526eV
Energy per atom: Epot =48.178eV Ekin = 6.344eV (T=527.707K) Etot = 54.522eV
Energy per atom: Epot =48.936eV Ekin = 5.592eV (T=465.200K) Etot = 54.528eV
Energy per atom: Epot =48.500eV Ekin = 6.025eV (T=501.160K) Etot = 54.525eV
Energy per atom: Epot =48.461eV Ekin = 6.065eV (T=504.501K) Etot = 54.526eV
Energy per atom: Epot =49.046eV Ekin = 5.483eV (T=456.147K) Etot = 54.530eV
Energy per atom: Epot =48.462eV Ekin = 6.065eV (T=504.525K) Etot = 54.527eV
Energy per atom: Epot =48.424eV Ekin = 6.101eV (T=507.541K) Etot = 54.526eV
Energy per atom: Epot =47.748eV Ekin = 6.773eV (T=563.426K) Etot = 54.521eV
Energy per atom: Epot =48.195eV Ekin = 6.330eV (T=526.560K) Etot = 54.525eV
Energy per atom: Epot =48.127eV Ekin = 6.396eV (T=532.081K) Etot = 54.523eV
Energy per atom: Epot =48.353eV Ekin = 6.172eV (T=513.407K) Etot = 54.524eV
Energy per atom: Epot =48.360eV Ekin = 6.168eV (T=513.071K) Etot = 54.528eV
Energy per atom: Epot =48.590eV Ekin = 5.937eV (T=493.916K) Etot = 54.527eV
Energy per atom: Epot =48.410eV Ekin = 6.115eV (T=508.691K) Etot = 54.525eV
Energy per atom: Epot =49.185eV Ekin = 5.343eV (T=444.467K) Etot = 54.528eV
Energy per atom: Epot =48.710eV Ekin = 5.815eV (T=483.744K) Etot = 54.525eV
Energy per atom: Epot =48.689eV Ekin = 5.836eV (T=485.444K) Etot = 54.525eV
Energy per atom: Epot =48.706eV Ekin = 5.819eV (T=484.022K) Etot = 54.524eV
After running the simulation, use Graphical user interface (GUI) to compare the resulting
trajectory with how it looks if you comment out either the line that says
Stationary(atoms), ZeroRotation(atoms) or both:
ase gui nanoparticleCu_NVE.traj
Try playing the movie with a high frame rate and set frame skipping to a low number. Can you spot the subtle difference?