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 = 155.222eV (T=300.212K) Etot = 152.817eV
Energy per atom: Epot =117.643eV Ekin = 35.966eV (T=69.562K) Etot = 153.610eV
Energy per atom: Epot =78.674eV Ekin = 74.797eV (T=144.664K) Etot = 153.471eV
Energy per atom: Epot =71.401eV Ekin = 81.919eV (T=158.438K) Etot = 153.320eV
Energy per atom: Epot =68.613eV Ekin = 84.651eV (T=163.722K) Etot = 153.263eV
Energy per atom: Epot =80.374eV Ekin = 73.057eV (T=141.299K) Etot = 153.431eV
Energy per atom: Epot =78.722eV Ekin = 74.702eV (T=144.479K) Etot = 153.424eV
Energy per atom: Epot =73.431eV Ekin = 79.895eV (T=154.525K) Etot = 153.327eV
Energy per atom: Epot =72.930eV Ekin = 80.406eV (T=155.513K) Etot = 153.336eV
Energy per atom: Epot =78.946eV Ekin = 74.468eV (T=144.027K) Etot = 153.413eV
Energy per atom: Epot =75.712eV Ekin = 77.655eV (T=150.192K) Etot = 153.368eV
Energy per atom: Epot =73.546eV Ekin = 79.798eV (T=154.336K) Etot = 153.344eV
Energy per atom: Epot =75.682eV Ekin = 77.688eV (T=150.256K) Etot = 153.370eV
Energy per atom: Epot =78.755eV Ekin = 74.629eV (T=144.340K) Etot = 153.384eV
Energy per atom: Epot =72.849eV Ekin = 80.499eV (T=155.692K) Etot = 153.348eV
Energy per atom: Epot =75.471eV Ekin = 77.900eV (T=150.665K) Etot = 153.371eV
Energy per atom: Epot =75.192eV Ekin = 78.174eV (T=151.196K) Etot = 153.366eV
Energy per atom: Epot =77.467eV Ekin = 75.902eV (T=146.800K) Etot = 153.369eV
Energy per atom: Epot =74.273eV Ekin = 79.087eV (T=152.961K) Etot = 153.360eV
Energy per atom: Epot =74.545eV Ekin = 78.814eV (T=152.433K) Etot = 153.359eV
Energy per atom: Epot =79.057eV Ekin = 74.330eV (T=143.761K) Etot = 153.388eV
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:102: 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 =600.539eV Ekin = 83.258eV (T=161.028K) Etot = 683.797eV
Energy per atom: Epot =672.269eV Ekin = 142.284eV (T=275.189K) Etot = 814.552eV
Energy per atom: Epot =729.019eV Ekin = 204.008eV (T=394.570K) Etot = 933.028eV
Energy per atom: Epot =787.703eV Ekin = 255.051eV (T=493.290K) Etot = 1042.754eV
Energy per atom: Epot =837.130eV Ekin = 298.768eV (T=577.843K) Etot = 1135.898eV
Energy per atom: Epot =883.211eV Ekin = 344.746eV (T=666.769K) Etot = 1227.957eV
Energy per atom: Epot =927.126eV Ekin = 385.033eV (T=744.687K) Etot = 1312.159eV
Energy per atom: Epot =963.901eV Ekin = 417.399eV (T=807.286K) Etot = 1381.300eV
Energy per atom: Epot =1007.180eV Ekin = 438.492eV (T=848.082K) Etot = 1445.672eV
Energy per atom: Epot =1048.149eV Ekin = 461.285eV (T=892.165K) Etot = 1509.434eV
Energy per atom: Epot =1075.718eV Ekin = 490.919eV (T=949.480K) Etot = 1566.637eV
Energy per atom: Epot =1103.559eV Ekin = 512.338eV (T=990.906K) Etot = 1615.897eV
Energy per atom: Epot =1142.486eV Ekin = 522.060eV (T=1009.710K) Etot = 1664.547eV
Energy per atom: Epot =1166.294eV Ekin = 546.638eV (T=1057.245K) Etot = 1712.932eV
Energy per atom: Epot =1196.219eV Ekin = 561.393eV (T=1085.783K) Etot = 1757.612eV
Energy per atom: Epot =1226.162eV Ekin = 564.247eV (T=1091.302K) Etot = 1790.409eV
Energy per atom: Epot =1250.083eV Ekin = 581.684eV (T=1125.028K) Etot = 1831.767eV
Energy per atom: Epot =1275.071eV Ekin = 604.316eV (T=1168.800K) Etot = 1879.387eV
Energy per atom: Epot =1312.857eV Ekin = 591.772eV (T=1144.539K) Etot = 1904.629eV
Energy per atom: Epot =1316.936eV Ekin = 608.397eV (T=1176.693K) Etot = 1925.333eV
Energy per atom: Epot =1341.840eV Ekin = 617.838eV (T=1194.953K) Etot = 1959.678eV
Energy per atom: Epot =1379.300eV Ekin = 610.542eV (T=1180.841K) Etot = 1989.842eV
Energy per atom: Epot =1373.296eV Ekin = 645.738eV (T=1248.914K) Etot = 2019.034eV
Energy per atom: Epot =1404.722eV Ekin = 649.345eV (T=1255.889K) Etot = 2054.067eV
Energy per atom: Epot =1429.869eV Ekin = 651.070eV (T=1259.226K) Etot = 2080.939eV
Energy per atom: Epot =1439.306eV Ekin = 668.612eV (T=1293.153K) Etot = 2107.917eV
Energy per atom: Epot =1471.972eV Ekin = 660.988eV (T=1278.409K) Etot = 2132.960eV
Energy per atom: Epot =1484.573eV Ekin = 667.990eV (T=1291.951K) Etot = 2152.563eV
Energy per atom: Epot =1494.808eV Ekin = 666.174eV (T=1288.438K) Etot = 2160.982eV
Energy per atom: Epot =1514.368eV Ekin = 669.617eV (T=1295.098K) Etot = 2183.985eV
Energy per atom: Epot =1526.131eV Ekin = 684.989eV (T=1324.828K) Etot = 2211.120eV
Energy per atom: Epot =1523.756eV Ekin = 692.884eV (T=1340.097K) Etot = 2216.639eV
Energy per atom: Epot =1539.527eV Ekin = 696.239eV (T=1346.586K) Etot = 2235.766eV
Energy per atom: Epot =1558.242eV Ekin = 695.299eV (T=1344.769K) Etot = 2253.542eV
Energy per atom: Epot =1570.948eV Ekin = 698.630eV (T=1351.211K) Etot = 2269.579eV
Energy per atom: Epot =1571.842eV Ekin = 714.042eV (T=1381.020K) Etot = 2285.885eV
Energy per atom: Epot =1586.488eV Ekin = 703.349eV (T=1360.337K) Etot = 2289.836eV
Energy per atom: Epot =1592.424eV Ekin = 713.682eV (T=1380.323K) Etot = 2306.106eV
Energy per atom: Epot =1603.517eV Ekin = 706.267eV (T=1365.982K) Etot = 2309.784eV
Energy per atom: Epot =1613.451eV Ekin = 708.338eV (T=1369.987K) Etot = 2321.789eV
Energy per atom: Epot =1630.543eV Ekin = 699.612eV (T=1353.111K) Etot = 2330.155eV
Energy per atom: Epot =1636.484eV Ekin = 708.832eV (T=1370.942K) Etot = 2345.316eV
Energy per atom: Epot =1640.873eV Ekin = 713.211eV (T=1379.413K) Etot = 2354.084eV
Energy per atom: Epot =1652.057eV Ekin = 708.723eV (T=1370.731K) Etot = 2360.780eV
Energy per atom: Epot =1650.568eV Ekin = 716.866eV (T=1386.481K) Etot = 2367.434eV
Energy per atom: Epot =1649.995eV Ekin = 723.772eV (T=1399.838K) Etot = 2373.768eV
Energy per atom: Epot =1667.034eV Ekin = 715.481eV (T=1383.803K) Etot = 2382.515eV
Energy per atom: Epot =1672.762eV Ekin = 730.187eV (T=1412.246K) Etot = 2402.949eV
Energy per atom: Epot =1664.501eV Ekin = 747.890eV (T=1446.483K) Etot = 2412.391eV
Energy per atom: Epot =1689.501eV Ekin = 737.721eV (T=1426.816K) Etot = 2427.222eV
Energy per atom: Epot =1702.525eV Ekin = 737.196eV (T=1425.800K) Etot = 2439.720eV
Energy per atom: Epot =1722.006eV Ekin = 713.690eV (T=1380.339K) Etot = 2435.696eV
Energy per atom: Epot =1733.734eV Ekin = 708.972eV (T=1371.213K) Etot = 2442.706eV
Energy per atom: Epot =1737.657eV Ekin = 713.205eV (T=1379.401K) Etot = 2450.863eV
Energy per atom: Epot =1740.839eV Ekin = 729.020eV (T=1409.988K) Etot = 2469.859eV
Energy per atom: Epot =1735.623eV Ekin = 741.578eV (T=1434.276K) Etot = 2477.201eV
Energy per atom: Epot =1749.719eV Ekin = 735.482eV (T=1422.487K) Etot = 2485.201eV
Energy per atom: Epot =1745.506eV Ekin = 741.172eV (T=1433.491K) Etot = 2486.678eV
Energy per atom: Epot =1748.125eV Ekin = 741.850eV (T=1434.802K) Etot = 2489.975eV
Energy per atom: Epot =1753.063eV Ekin = 730.663eV (T=1413.165K) Etot = 2483.726eV
Energy per atom: Epot =1751.920eV Ekin = 750.404eV (T=1451.346K) Etot = 2502.324eV
Energy per atom: Epot =1769.040eV Ekin = 736.773eV (T=1424.983K) Etot = 2505.812eV
Energy per atom: Epot =1772.561eV Ekin = 736.222eV (T=1423.918K) Etot = 2508.784eV
Energy per atom: Epot =1791.106eV Ekin = 729.858eV (T=1411.609K) Etot = 2520.964eV
Energy per atom: Epot =1789.319eV Ekin = 733.853eV (T=1419.335K) Etot = 2523.172eV
Energy per atom: Epot =1807.372eV Ekin = 727.328eV (T=1406.715K) Etot = 2534.700eV
Energy per atom: Epot =1798.754eV Ekin = 737.104eV (T=1425.623K) Etot = 2535.858eV
Energy per atom: Epot =1811.371eV Ekin = 729.227eV (T=1410.388K) Etot = 2540.598eV
Energy per atom: Epot =1805.200eV Ekin = 732.786eV (T=1417.272K) Etot = 2537.986eV
Energy per atom: Epot =1799.025eV Ekin = 742.535eV (T=1436.128K) Etot = 2541.560eV
Energy per atom: Epot =1819.555eV Ekin = 735.956eV (T=1423.402K) Etot = 2555.510eV
Energy per atom: Epot =1830.949eV Ekin = 729.828eV (T=1411.551K) Etot = 2560.777eV
Energy per atom: Epot =1835.680eV Ekin = 730.244eV (T=1412.356K) Etot = 2565.924eV
Energy per atom: Epot =1840.173eV Ekin = 722.327eV (T=1397.042K) Etot = 2562.500eV
Energy per atom: Epot =1846.313eV Ekin = 737.507eV (T=1426.403K) Etot = 2583.820eV
Energy per atom: Epot =1845.397eV Ekin = 740.252eV (T=1431.712K) Etot = 2585.649eV
Energy per atom: Epot =1847.918eV Ekin = 744.716eV (T=1440.346K) Etot = 2592.634eV
Energy per atom: Epot =1851.969eV Ekin = 756.019eV (T=1462.207K) Etot = 2607.988eV
Energy per atom: Epot =1863.399eV Ekin = 753.922eV (T=1458.150K) Etot = 2617.321eV
Energy per atom: Epot =1862.979eV Ekin = 752.889eV (T=1456.153K) Etot = 2615.868eV
Energy per atom: Epot =1866.204eV Ekin = 748.497eV (T=1447.658K) Etot = 2614.701eV
Energy per atom: Epot =1867.472eV Ekin = 745.809eV (T=1442.460K) Etot = 2613.281eV
Energy per atom: Epot =1862.419eV Ekin = 751.612eV (T=1453.684K) Etot = 2614.032eV
Energy per atom: Epot =1869.933eV Ekin = 751.563eV (T=1453.588K) Etot = 2621.496eV
Energy per atom: Epot =1873.891eV Ekin = 747.676eV (T=1446.070K) Etot = 2621.567eV
Energy per atom: Epot =1871.112eV Ekin = 760.909eV (T=1471.664K) Etot = 2632.021eV
Energy per atom: Epot =1877.336eV Ekin = 761.305eV (T=1472.429K) Etot = 2638.641eV
Energy per atom: Epot =1901.784eV Ekin = 752.465eV (T=1455.332K) Etot = 2654.249eV
Energy per atom: Epot =1905.253eV Ekin = 752.024eV (T=1454.480K) Etot = 2657.277eV
Energy per atom: Epot =1910.270eV Ekin = 755.229eV (T=1460.678K) Etot = 2665.499eV
Energy per atom: Epot =1907.937eV Ekin = 761.634eV (T=1473.067K) Etot = 2669.572eV
Energy per atom: Epot =1914.981eV Ekin = 750.835eV (T=1452.180K) Etot = 2665.816eV
Energy per atom: Epot =1916.436eV Ekin = 759.749eV (T=1469.421K) Etot = 2676.186eV
Energy per atom: Epot =1919.962eV Ekin = 752.532eV (T=1455.463K) Etot = 2672.494eV
Energy per atom: Epot =1927.173eV Ekin = 742.395eV (T=1435.857K) Etot = 2669.569eV
Energy per atom: Epot =1916.041eV Ekin = 756.179eV (T=1462.516K) Etot = 2672.220eV
Energy per atom: Epot =1907.088eV Ekin = 764.728eV (T=1479.051K) Etot = 2671.816eV
Energy per atom: Epot =1929.148eV Ekin = 744.529eV (T=1439.985K) Etot = 2673.677eV
Energy per atom: Epot =1910.106eV Ekin = 764.044eV (T=1477.728K) Etot = 2674.151eV
Energy per atom: Epot =1930.757eV Ekin = 742.418eV (T=1435.902K) Etot = 2673.175eV
Energy per atom: Epot =1925.992eV Ekin = 765.757eV (T=1481.041K) Etot = 2691.750eV
Energy per atom: Epot =1940.151eV Ekin = 763.859eV (T=1477.370K) Etot = 2704.010eV
Energy per atom: Epot =1923.658eV Ekin = 777.976eV (T=1504.674K) Etot = 2701.634eV
Energy per atom: Epot =1948.659eV Ekin = 757.238eV (T=1464.564K) Etot = 2705.896eV
Energy per atom: Epot =1944.553eV Ekin = 761.435eV (T=1472.681K) Etot = 2705.988eV
Energy per atom: Epot =1953.272eV Ekin = 749.171eV (T=1448.962K) Etot = 2702.443eV
Energy per atom: Epot =1959.024eV Ekin = 755.782eV (T=1461.748K) Etot = 2714.806eV
Energy per atom: Epot =1973.191eV Ekin = 756.964eV (T=1464.034K) Etot = 2730.155eV
Energy per atom: Epot =1965.280eV Ekin = 773.703eV (T=1496.409K) Etot = 2738.983eV
Energy per atom: Epot =1978.956eV Ekin = 767.237eV (T=1483.904K) Etot = 2746.194eV
Energy per atom: Epot =1979.444eV Ekin = 775.637eV (T=1500.150K) Etot = 2755.081eV
Energy per atom: Epot =1991.907eV Ekin = 766.845eV (T=1483.145K) Etot = 2758.752eV
Energy per atom: Epot =1991.137eV Ekin = 770.963eV (T=1491.110K) Etot = 2762.100eV
Energy per atom: Epot =1981.434eV Ekin = 782.428eV (T=1513.283K) Etot = 2763.862eV
Energy per atom: Epot =1989.018eV Ekin = 770.768eV (T=1490.732K) Etot = 2759.786eV
Energy per atom: Epot =1977.682eV Ekin = 780.041eV (T=1508.667K) Etot = 2757.723eV
Energy per atom: Epot =1984.080eV Ekin = 778.604eV (T=1505.887K) Etot = 2762.684eV
Energy per atom: Epot =1988.725eV Ekin = 780.338eV (T=1509.242K) Etot = 2769.063eV
Energy per atom: Epot =1986.877eV Ekin = 785.718eV (T=1519.647K) Etot = 2772.595eV
Energy per atom: Epot =1995.099eV Ekin = 776.843eV (T=1502.482K) Etot = 2771.942eV
Energy per atom: Epot =1998.937eV Ekin = 773.247eV (T=1495.526K) Etot = 2772.183eV
Energy per atom: Epot =1990.852eV Ekin = 787.378eV (T=1522.858K) Etot = 2778.231eV
Energy per atom: Epot =1982.486eV Ekin = 782.578eV (T=1513.574K) Etot = 2765.064eV
Energy per atom: Epot =1995.493eV Ekin = 775.662eV (T=1500.198K) Etot = 2771.155eV
Energy per atom: Epot =1986.610eV Ekin = 770.834eV (T=1490.859K) Etot = 2757.444eV
Energy per atom: Epot =2006.981eV Ekin = 756.642eV (T=1463.412K) Etot = 2763.623eV
Energy per atom: Epot =1999.333eV Ekin = 769.150eV (T=1487.603K) Etot = 2768.483eV
Energy per atom: Epot =1994.653eV Ekin = 787.824eV (T=1523.721K) Etot = 2782.478eV
Energy per atom: Epot =2004.481eV Ekin = 775.824eV (T=1500.511K) Etot = 2780.305eV
Energy per atom: Epot =2003.229eV Ekin = 774.898eV (T=1498.720K) Etot = 2778.127eV
Energy per atom: Epot =2007.855eV Ekin = 774.006eV (T=1496.995K) Etot = 2781.861eV
Energy per atom: Epot =2003.611eV Ekin = 780.057eV (T=1508.697K) Etot = 2783.668eV
Energy per atom: Epot =2019.501eV Ekin = 769.446eV (T=1488.176K) Etot = 2788.947eV
Energy per atom: Epot =2008.019eV Ekin = 770.948eV (T=1491.081K) Etot = 2778.967eV
Energy per atom: Epot =2004.822eV Ekin = 779.182eV (T=1507.006K) Etot = 2784.004eV
Energy per atom: Epot =2015.897eV Ekin = 773.179eV (T=1495.396K) Etot = 2789.077eV
Energy per atom: Epot =2005.559eV Ekin = 781.858eV (T=1512.182K) Etot = 2787.418eV
Energy per atom: Epot =2014.900eV Ekin = 770.179eV (T=1489.594K) Etot = 2785.079eV
Energy per atom: Epot =2018.741eV Ekin = 783.715eV (T=1515.773K) Etot = 2802.456eV
Energy per atom: Epot =2006.564eV Ekin = 791.067eV (T=1529.992K) Etot = 2797.631eV
Energy per atom: Epot =2015.580eV Ekin = 779.367eV (T=1507.364K) Etot = 2794.947eV
Energy per atom: Epot =2007.272eV Ekin = 790.238eV (T=1528.389K) Etot = 2797.509eV
Energy per atom: Epot =2008.241eV Ekin = 781.984eV (T=1512.425K) Etot = 2790.224eV
Energy per atom: Epot =2012.960eV Ekin = 776.718eV (T=1502.240K) Etot = 2789.678eV
Energy per atom: Epot =2005.593eV Ekin = 782.468eV (T=1513.361K) Etot = 2788.061eV
Energy per atom: Epot =1999.347eV Ekin = 786.735eV (T=1521.613K) Etot = 2786.081eV
Energy per atom: Epot =2010.125eV Ekin = 767.877eV (T=1485.141K) Etot = 2778.002eV
Energy per atom: Epot =2001.139eV Ekin = 787.310eV (T=1522.726K) Etot = 2788.449eV
Energy per atom: Epot =1997.914eV Ekin = 796.706eV (T=1540.899K) Etot = 2794.620eV
Energy per atom: Epot =2018.914eV Ekin = 769.732eV (T=1488.728K) Etot = 2788.646eV
Energy per atom: Epot =2017.959eV Ekin = 774.940eV (T=1498.802K) Etot = 2792.900eV
Energy per atom: Epot =2011.077eV Ekin = 779.126eV (T=1506.897K) Etot = 2790.202eV
Energy per atom: Epot =2006.798eV Ekin = 783.353eV (T=1515.073K) Etot = 2790.152eV
Energy per atom: Epot =2007.720eV Ekin = 778.236eV (T=1505.176K) Etot = 2785.955eV
Energy per atom: Epot =2012.446eV Ekin = 773.243eV (T=1495.519K) Etot = 2785.689eV
Energy per atom: Epot =2009.258eV Ekin = 775.006eV (T=1498.929K) Etot = 2784.264eV
Energy per atom: Epot =2002.526eV Ekin = 763.981eV (T=1477.605K) Etot = 2766.507eV
Energy per atom: Epot =1999.467eV Ekin = 768.311eV (T=1485.980K) Etot = 2767.778eV
Energy per atom: Epot =2010.358eV Ekin = 755.037eV (T=1460.308K) Etot = 2765.395eV
Energy per atom: Epot =1998.571eV Ekin = 764.832eV (T=1479.252K) Etot = 2763.403eV
Energy per atom: Epot =2002.831eV Ekin = 763.553eV (T=1476.778K) Etot = 2766.384eV
Energy per atom: Epot =2004.356eV Ekin = 770.007eV (T=1489.261K) Etot = 2774.363eV
Energy per atom: Epot =1993.744eV Ekin = 782.019eV (T=1512.493K) Etot = 2775.763eV
Energy per atom: Epot =1995.594eV Ekin = 768.569eV (T=1486.479K) Etot = 2764.163eV
Energy per atom: Epot =2007.771eV Ekin = 759.916eV (T=1469.745K) Etot = 2767.687eV
Energy per atom: Epot =2003.142eV Ekin = 767.201eV (T=1483.834K) Etot = 2770.344eV
Energy per atom: Epot =2004.762eV Ekin = 765.904eV (T=1481.325K) Etot = 2770.666eV
Energy per atom: Epot =2000.216eV Ekin = 772.484eV (T=1494.051K) Etot = 2772.700eV
Energy per atom: Epot =1996.585eV Ekin = 767.139eV (T=1483.713K) Etot = 2763.724eV
Energy per atom: Epot =1996.273eV Ekin = 765.209eV (T=1479.980K) Etot = 2761.482eV
Energy per atom: Epot =1992.475eV Ekin = 765.130eV (T=1479.828K) Etot = 2757.605eV
Energy per atom: Epot =1976.996eV Ekin = 770.506eV (T=1490.226K) Etot = 2747.502eV
Energy per atom: Epot =1983.213eV Ekin = 763.720eV (T=1477.101K) Etot = 2746.933eV
Energy per atom: Epot =1982.862eV Ekin = 762.075eV (T=1473.920K) Etot = 2744.938eV
Energy per atom: Epot =1967.819eV Ekin = 778.069eV (T=1504.852K) Etot = 2745.887eV
Energy per atom: Epot =1974.314eV Ekin = 771.052eV (T=1491.283K) Etot = 2745.367eV
Energy per atom: Epot =1972.413eV Ekin = 769.483eV (T=1488.247K) Etot = 2741.896eV
Energy per atom: Epot =1965.298eV Ekin = 785.340eV (T=1518.916K) Etot = 2750.638eV
Energy per atom: Epot =1972.158eV Ekin = 770.755eV (T=1490.707K) Etot = 2742.912eV
Energy per atom: Epot =1985.029eV Ekin = 762.276eV (T=1474.307K) Etot = 2747.305eV
Energy per atom: Epot =1982.956eV Ekin = 763.744eV (T=1477.148K) Etot = 2746.700eV
Energy per atom: Epot =1994.257eV Ekin = 755.244eV (T=1460.708K) Etot = 2749.501eV
Energy per atom: Epot =1985.223eV Ekin = 770.612eV (T=1490.430K) Etot = 2755.835eV
Energy per atom: Epot =1979.411eV Ekin = 773.479eV (T=1495.976K) Etot = 2752.890eV
Energy per atom: Epot =1991.584eV Ekin = 761.951eV (T=1473.679K) Etot = 2753.535eV
Energy per atom: Epot =1973.455eV Ekin = 784.554eV (T=1517.396K) Etot = 2758.009eV
Energy per atom: Epot =1986.900eV Ekin = 764.223eV (T=1478.074K) Etot = 2751.123eV
Energy per atom: Epot =1988.478eV Ekin = 763.644eV (T=1476.955K) Etot = 2752.123eV
Energy per atom: Epot =1974.100eV Ekin = 780.127eV (T=1508.834K) Etot = 2754.227eV
Energy per atom: Epot =1964.010eV Ekin = 789.913eV (T=1527.760K) Etot = 2753.923eV
Energy per atom: Epot =1976.780eV Ekin = 775.743eV (T=1500.355K) Etot = 2752.523eV
Energy per atom: Epot =1993.377eV Ekin = 754.825eV (T=1459.897K) Etot = 2748.202eV
Energy per atom: Epot =1985.973eV Ekin = 764.207eV (T=1478.043K) Etot = 2750.180eV
Energy per atom: Epot =1978.429eV Ekin = 779.183eV (T=1507.007K) Etot = 2757.612eV
Energy per atom: Epot =1990.697eV Ekin = 761.351eV (T=1472.519K) Etot = 2752.048eV
Energy per atom: Epot =1993.831eV Ekin = 743.068eV (T=1437.158K) Etot = 2736.899eV
Energy per atom: Epot =1987.894eV Ekin = 752.442eV (T=1455.289K) Etot = 2740.336eV
Energy per atom: Epot =1986.534eV Ekin = 764.167eV (T=1477.965K) Etot = 2750.701eV
Energy per atom: Epot =1984.039eV Ekin = 772.213eV (T=1493.527K) Etot = 2756.252eV
Energy per atom: Epot =1989.274eV Ekin = 761.909eV (T=1473.599K) Etot = 2751.183eV
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] 15:07:59 43.457006 1.0818
BFGSLineSearch: 1[ 1] 15:07:59 42.347659 0.2273
BFGSLineSearch: 2[ 2] 15:07:59 42.108454 0.1349
BFGSLineSearch: 3[ 3] 15:07:59 41.964817 0.1138
BFGSLineSearch: 4[ 4] 15:07:59 41.924933 0.0683
BFGSLineSearch: 5[ 5] 15:07:59 41.915346 0.0225
BFGSLineSearch: 6[ 6] 15:07:59 41.914920 0.0059
BFGSLineSearch: 7[ 7] 15:07:59 41.914872 0.0023
BFGSLineSearch: 8[ 9] 15:07:59 41.914855 0.0023
BFGSLineSearch: 9[ 10] 15:07:59 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 = 16.018eV (T=1332.520K) Etot = 57.933eV
Energy per atom: Epot =50.650eV Ekin = 7.334eV (T=610.065K) Etot = 57.984eV
Energy per atom: Epot =51.604eV Ekin = 6.388eV (T=531.421K) Etot = 57.993eV
Energy per atom: Epot =51.798eV Ekin = 6.191eV (T=514.970K) Etot = 57.989eV
Energy per atom: Epot =52.210eV Ekin = 5.783eV (T=481.063K) Etot = 57.993eV
Energy per atom: Epot =50.921eV Ekin = 7.071eV (T=588.246K) Etot = 57.992eV
Energy per atom: Epot =49.940eV Ekin = 8.045eV (T=669.211K) Etot = 57.985eV
Energy per atom: Epot =49.434eV Ekin = 8.544eV (T=710.752K) Etot = 57.978eV
Energy per atom: Epot =50.713eV Ekin = 7.271eV (T=604.855K) Etot = 57.984eV
Energy per atom: Epot =51.600eV Ekin = 6.392eV (T=531.695K) Etot = 57.992eV
Energy per atom: Epot =51.765eV Ekin = 6.226eV (T=517.900K) Etot = 57.991eV
Energy per atom: Epot =52.365eV Ekin = 5.630eV (T=468.340K) Etot = 57.995eV
Energy per atom: Epot =50.588eV Ekin = 7.396eV (T=615.224K) Etot = 57.983eV
Energy per atom: Epot =50.796eV Ekin = 7.190eV (T=598.100K) Etot = 57.986eV
Energy per atom: Epot =50.424eV Ekin = 7.562eV (T=629.097K) Etot = 57.986eV
Energy per atom: Epot =50.694eV Ekin = 7.295eV (T=606.811K) Etot = 57.988eV
Energy per atom: Epot =51.025eV Ekin = 6.970eV (T=579.798K) Etot = 57.994eV
Energy per atom: Epot =51.800eV Ekin = 6.192eV (T=515.114K) Etot = 57.992eV
Energy per atom: Epot =50.720eV Ekin = 7.263eV (T=604.185K) Etot = 57.983eV
Energy per atom: Epot =50.768eV Ekin = 7.213eV (T=600.066K) Etot = 57.982eV
Energy per atom: Epot =50.503eV Ekin = 7.482eV (T=622.374K) Etot = 57.985eV
Energy per atom: Epot =50.008eV Ekin = 7.975eV (T=663.452K) Etot = 57.983eV
Energy per atom: Epot =50.751eV Ekin = 7.237eV (T=602.011K) Etot = 57.988eV
Energy per atom: Epot =51.462eV Ekin = 6.526eV (T=542.898K) Etot = 57.988eV
Energy per atom: Epot =50.407eV Ekin = 7.574eV (T=630.080K) Etot = 57.981eV
Energy per atom: Epot =50.453eV Ekin = 7.526eV (T=626.083K) Etot = 57.979eV
Energy per atom: Epot =50.953eV Ekin = 7.032eV (T=584.955K) Etot = 57.985eV
Energy per atom: Epot =51.024eV Ekin = 6.968eV (T=579.642K) Etot = 57.992eV
Energy per atom: Epot =50.298eV Ekin = 7.686eV (T=639.334K) Etot = 57.984eV
Energy per atom: Epot =50.909eV Ekin = 7.082eV (T=589.119K) Etot = 57.991eV
Energy per atom: Epot =50.004eV Ekin = 7.982eV (T=664.028K) Etot = 57.986eV
Energy per atom: Epot =50.988eV Ekin = 6.996eV (T=581.986K) Etot = 57.984eV
Energy per atom: Epot =50.452eV Ekin = 7.531eV (T=626.440K) Etot = 57.983eV
Energy per atom: Epot =51.187eV Ekin = 6.801eV (T=565.724K) Etot = 57.987eV
Energy per atom: Epot =51.325eV Ekin = 6.664eV (T=554.391K) Etot = 57.989eV
Energy per atom: Epot =51.150eV Ekin = 6.835eV (T=568.611K) Etot = 57.986eV
Energy per atom: Epot =51.722eV Ekin = 6.269eV (T=521.464K) Etot = 57.991eV
Energy per atom: Epot =52.340eV Ekin = 5.654eV (T=470.325K) Etot = 57.994eV
Energy per atom: Epot =49.954eV Ekin = 8.026eV (T=667.658K) Etot = 57.980eV
Energy per atom: Epot =50.122eV Ekin = 7.858eV (T=653.679K) Etot = 57.980eV
Energy per atom: Epot =50.077eV Ekin = 7.910eV (T=658.015K) Etot = 57.987eV
Energy per atom: Epot =51.698eV Ekin = 6.294eV (T=523.583K) Etot = 57.992eV
Energy per atom: Epot =51.955eV Ekin = 6.035eV (T=502.042K) Etot = 57.990eV
Energy per atom: Epot =50.676eV Ekin = 7.310eV (T=608.058K) Etot = 57.986eV
Energy per atom: Epot =50.623eV Ekin = 7.356eV (T=611.905K) Etot = 57.979eV
Energy per atom: Epot =49.911eV Ekin = 8.068eV (T=671.145K) Etot = 57.979eV
Energy per atom: Epot =50.561eV Ekin = 7.425eV (T=617.693K) Etot = 57.986eV
Energy per atom: Epot =51.162eV Ekin = 6.823eV (T=567.591K) Etot = 57.985eV
Energy per atom: Epot =50.782eV Ekin = 7.204eV (T=599.275K) Etot = 57.986eV
Energy per atom: Epot =51.170eV Ekin = 6.822eV (T=567.500K) Etot = 57.992eV
Energy per atom: Epot =50.743eV Ekin = 7.250eV (T=603.133K) Etot = 57.993eV
Energy per atom: Epot =49.893eV Ekin = 8.084eV (T=672.474K) Etot = 57.977eV
Energy per atom: Epot =50.830eV Ekin = 7.155eV (T=595.220K) Etot = 57.986eV
Energy per atom: Epot =49.137eV Ekin = 8.845eV (T=735.813K) Etot = 57.983eV
Energy per atom: Epot =51.054eV Ekin = 6.940eV (T=577.297K) Etot = 57.994eV
Energy per atom: Epot =51.124eV Ekin = 6.866eV (T=571.164K) Etot = 57.990eV
Energy per atom: Epot =50.508eV Ekin = 7.476eV (T=621.905K) Etot = 57.985eV
Energy per atom: Epot =50.067eV Ekin = 7.914eV (T=658.362K) Etot = 57.982eV
Energy per atom: Epot =50.007eV Ekin = 7.975eV (T=663.380K) Etot = 57.982eV
Energy per atom: Epot =51.164eV Ekin = 6.823eV (T=567.590K) Etot = 57.987eV
Energy per atom: Epot =50.684eV Ekin = 7.300eV (T=607.267K) Etot = 57.985eV
Energy per atom: Epot =50.170eV Ekin = 7.816eV (T=650.168K) Etot = 57.985eV
Energy per atom: Epot =49.645eV Ekin = 8.334eV (T=693.264K) Etot = 57.979eV
Energy per atom: Epot =50.576eV Ekin = 7.408eV (T=616.287K) Etot = 57.984eV
Energy per atom: Epot =50.579eV Ekin = 7.405eV (T=615.979K) Etot = 57.984eV
Energy per atom: Epot =50.299eV Ekin = 7.690eV (T=639.711K) Etot = 57.989eV
Energy per atom: Epot =50.416eV Ekin = 7.573eV (T=629.993K) Etot = 57.989eV
Energy per atom: Epot =50.167eV Ekin = 7.814eV (T=649.979K) Etot = 57.981eV
Energy per atom: Epot =50.720eV Ekin = 7.268eV (T=604.641K) Etot = 57.988eV
Energy per atom: Epot =50.356eV Ekin = 7.632eV (T=634.843K) Etot = 57.988eV
Energy per atom: Epot =49.969eV Ekin = 8.018eV (T=667.004K) Etot = 57.987eV
Energy per atom: Epot =50.310eV Ekin = 7.677eV (T=638.651K) Etot = 57.988eV
Energy per atom: Epot =51.074eV Ekin = 6.914eV (T=575.139K) Etot = 57.988eV
Energy per atom: Epot =50.862eV Ekin = 7.131eV (T=593.182K) Etot = 57.992eV
Energy per atom: Epot =50.821eV Ekin = 7.169eV (T=596.334K) Etot = 57.989eV
Energy per atom: Epot =50.318eV Ekin = 7.660eV (T=637.223K) Etot = 57.978eV
Energy per atom: Epot =50.877eV Ekin = 7.105eV (T=591.074K) Etot = 57.983eV
Energy per atom: Epot =50.364eV Ekin = 7.624eV (T=634.224K) Etot = 57.988eV
Energy per atom: Epot =50.001eV Ekin = 7.981eV (T=663.885K) Etot = 57.982eV
Energy per atom: Epot =51.170eV Ekin = 6.825eV (T=567.774K) Etot = 57.995eV
Energy per atom: Epot =50.462eV Ekin = 7.527eV (T=626.144K) Etot = 57.989eV
Energy per atom: Epot =49.937eV Ekin = 8.044eV (T=669.162K) Etot = 57.981eV
Energy per atom: Epot =50.832eV Ekin = 7.155eV (T=595.190K) Etot = 57.987eV
Energy per atom: Epot =50.670eV Ekin = 7.318eV (T=608.743K) Etot = 57.988eV
Energy per atom: Epot =50.228eV Ekin = 7.757eV (T=645.302K) Etot = 57.985eV
Energy per atom: Epot =50.896eV Ekin = 7.092eV (T=589.928K) Etot = 57.988eV
Energy per atom: Epot =50.624eV Ekin = 7.364eV (T=612.546K) Etot = 57.987eV
Energy per atom: Epot =49.991eV Ekin = 7.994eV (T=664.983K) Etot = 57.984eV
Energy per atom: Epot =50.283eV Ekin = 7.702eV (T=640.712K) Etot = 57.985eV
Energy per atom: Epot =50.424eV Ekin = 7.563eV (T=629.103K) Etot = 57.987eV
Energy per atom: Epot =50.925eV Ekin = 7.066eV (T=587.757K) Etot = 57.991eV
Energy per atom: Epot =49.842eV Ekin = 8.140eV (T=677.170K) Etot = 57.982eV
Energy per atom: Epot =49.969eV Ekin = 8.018eV (T=666.968K) Etot = 57.987eV
Energy per atom: Epot =50.718eV Ekin = 7.275eV (T=605.217K) Etot = 57.994eV
Energy per atom: Epot =50.214eV Ekin = 7.778eV (T=647.054K) Etot = 57.992eV
Energy per atom: Epot =49.704eV Ekin = 8.284eV (T=689.081K) Etot = 57.988eV
Energy per atom: Epot =49.530eV Ekin = 8.456eV (T=703.446K) Etot = 57.986eV
Energy per atom: Epot =48.929eV Ekin = 9.051eV (T=752.910K) Etot = 57.980eV
Energy per atom: Epot =50.187eV Ekin = 7.792eV (T=648.206K) Etot = 57.979eV
Energy per atom: Epot =49.912eV Ekin = 8.069eV (T=671.252K) Etot = 57.981eV
Energy per atom: Epot =51.008eV Ekin = 6.983eV (T=580.894K) Etot = 57.991eV
Energy per atom: Epot =49.923eV Ekin = 8.061eV (T=670.534K) Etot = 57.983eV
Energy per atom: Epot =50.673eV Ekin = 7.315eV (T=608.502K) Etot = 57.988eV
Energy per atom: Epot =49.662eV Ekin = 8.323eV (T=692.339K) Etot = 57.985eV
Energy per atom: Epot =49.457eV Ekin = 8.528eV (T=709.429K) Etot = 57.985eV
Energy per atom: Epot =49.526eV Ekin = 8.460eV (T=703.748K) Etot = 57.986eV
Energy per atom: Epot =49.997eV Ekin = 7.992eV (T=664.799K) Etot = 57.988eV
Energy per atom: Epot =50.600eV Ekin = 7.391eV (T=614.801K) Etot = 57.991eV
Energy per atom: Epot =50.714eV Ekin = 7.274eV (T=605.120K) Etot = 57.988eV
Energy per atom: Epot =50.677eV Ekin = 7.307eV (T=607.806K) Etot = 57.984eV
Energy per atom: Epot =50.350eV Ekin = 7.634eV (T=635.018K) Etot = 57.984eV
Energy per atom: Epot =50.511eV Ekin = 7.476eV (T=621.897K) Etot = 57.987eV
Energy per atom: Epot =51.258eV Ekin = 6.728eV (T=559.643K) Etot = 57.986eV
Energy per atom: Epot =50.951eV Ekin = 7.037eV (T=585.357K) Etot = 57.987eV
Energy per atom: Epot =50.477eV Ekin = 7.509eV (T=624.684K) Etot = 57.986eV
Energy per atom: Epot =50.981eV Ekin = 7.010eV (T=583.153K) Etot = 57.991eV
Energy per atom: Epot =50.942eV Ekin = 7.040eV (T=585.651K) Etot = 57.982eV
Energy per atom: Epot =49.887eV Ekin = 8.090eV (T=672.972K) Etot = 57.977eV
Energy per atom: Epot =49.720eV Ekin = 8.261eV (T=687.202K) Etot = 57.981eV
Energy per atom: Epot =50.291eV Ekin = 7.696eV (T=640.187K) Etot = 57.986eV
Energy per atom: Epot =49.958eV Ekin = 8.019eV (T=667.067K) Etot = 57.976eV
Energy per atom: Epot =49.260eV Ekin = 8.716eV (T=725.087K) Etot = 57.976eV
Energy per atom: Epot =50.550eV Ekin = 7.436eV (T=618.548K) Etot = 57.986eV
Energy per atom: Epot =49.761eV Ekin = 8.223eV (T=684.075K) Etot = 57.984eV
Energy per atom: Epot =49.993eV Ekin = 7.994eV (T=664.959K) Etot = 57.987eV
Energy per atom: Epot =50.531eV Ekin = 7.456eV (T=620.261K) Etot = 57.988eV
Energy per atom: Epot =50.297eV Ekin = 7.688eV (T=639.531K) Etot = 57.984eV
Energy per atom: Epot =50.387eV Ekin = 7.603eV (T=632.452K) Etot = 57.989eV
Energy per atom: Epot =49.614eV Ekin = 8.370eV (T=696.288K) Etot = 57.984eV
Energy per atom: Epot =49.728eV Ekin = 8.258eV (T=686.919K) Etot = 57.986eV
Energy per atom: Epot =50.096eV Ekin = 7.893eV (T=656.605K) Etot = 57.989eV
Energy per atom: Epot =50.555eV Ekin = 7.432eV (T=618.211K) Etot = 57.987eV
Energy per atom: Epot =49.878eV Ekin = 8.102eV (T=674.001K) Etot = 57.981eV
Energy per atom: Epot =50.309eV Ekin = 7.674eV (T=638.347K) Etot = 57.982eV
Energy per atom: Epot =50.120eV Ekin = 7.866eV (T=654.327K) Etot = 57.986eV
Energy per atom: Epot =50.166eV Ekin = 7.817eV (T=650.234K) Etot = 57.983eV
Energy per atom: Epot =48.811eV Ekin = 9.167eV (T=762.556K) Etot = 57.978eV
Energy per atom: Epot =49.788eV Ekin = 8.198eV (T=681.922K) Etot = 57.985eV
Energy per atom: Epot =49.524eV Ekin = 8.461eV (T=703.873K) Etot = 57.986eV
Energy per atom: Epot =49.570eV Ekin = 8.416eV (T=700.074K) Etot = 57.985eV
Energy per atom: Epot =50.453eV Ekin = 7.536eV (T=626.887K) Etot = 57.989eV
Energy per atom: Epot =50.870eV Ekin = 7.118eV (T=592.089K) Etot = 57.988eV
Energy per atom: Epot =50.212eV Ekin = 7.770eV (T=646.378K) Etot = 57.983eV
Energy per atom: Epot =50.912eV Ekin = 7.078eV (T=588.820K) Etot = 57.991eV
Energy per atom: Epot =50.264eV Ekin = 7.728eV (T=642.848K) Etot = 57.991eV
Energy per atom: Epot =50.375eV Ekin = 7.609eV (T=632.992K) Etot = 57.985eV
Energy per atom: Epot =49.759eV Ekin = 8.222eV (T=683.994K) Etot = 57.982eV
Energy per atom: Epot =50.284eV Ekin = 7.700eV (T=640.506K) Etot = 57.984eV
Energy per atom: Epot =49.671eV Ekin = 8.316eV (T=691.759K) Etot = 57.986eV
Energy per atom: Epot =49.359eV Ekin = 8.623eV (T=717.333K) Etot = 57.982eV
Energy per atom: Epot =50.895eV Ekin = 7.098eV (T=590.419K) Etot = 57.992eV
Energy per atom: Epot =50.399eV Ekin = 7.592eV (T=631.560K) Etot = 57.991eV
Energy per atom: Epot =50.302eV Ekin = 7.682eV (T=639.074K) Etot = 57.985eV
Energy per atom: Epot =49.961eV Ekin = 8.024eV (T=667.498K) Etot = 57.985eV
Energy per atom: Epot =49.597eV Ekin = 8.388eV (T=697.764K) Etot = 57.985eV
Energy per atom: Epot =50.134eV Ekin = 7.851eV (T=653.126K) Etot = 57.985eV
Energy per atom: Epot =50.136eV Ekin = 7.853eV (T=653.264K) Etot = 57.989eV
Energy per atom: Epot =50.283eV Ekin = 7.704eV (T=640.846K) Etot = 57.987eV
Energy per atom: Epot =50.778eV Ekin = 7.210eV (T=599.779K) Etot = 57.988eV
Energy per atom: Epot =50.363eV Ekin = 7.630eV (T=634.678K) Etot = 57.993eV
Energy per atom: Epot =49.831eV Ekin = 8.156eV (T=678.473K) Etot = 57.987eV
Energy per atom: Epot =49.473eV Ekin = 8.508eV (T=707.736K) Etot = 57.981eV
Energy per atom: Epot =49.323eV Ekin = 8.657eV (T=720.115K) Etot = 57.980eV
Energy per atom: Epot =50.054eV Ekin = 7.931eV (T=659.775K) Etot = 57.986eV
Energy per atom: Epot =49.706eV Ekin = 8.278eV (T=688.630K) Etot = 57.984eV
Energy per atom: Epot =50.673eV Ekin = 7.312eV (T=608.256K) Etot = 57.985eV
Energy per atom: Epot =50.074eV Ekin = 7.903eV (T=657.436K) Etot = 57.977eV
Energy per atom: Epot =49.772eV Ekin = 8.212eV (T=683.101K) Etot = 57.984eV
Energy per atom: Epot =50.023eV Ekin = 7.965eV (T=662.545K) Etot = 57.988eV
Energy per atom: Epot =50.260eV Ekin = 7.726eV (T=642.667K) Etot = 57.986eV
Energy per atom: Epot =49.590eV Ekin = 8.393eV (T=698.167K) Etot = 57.982eV
Energy per atom: Epot =50.375eV Ekin = 7.613eV (T=633.296K) Etot = 57.987eV
Energy per atom: Epot =49.717eV Ekin = 8.269eV (T=687.849K) Etot = 57.986eV
Energy per atom: Epot =49.604eV Ekin = 8.379eV (T=696.986K) Etot = 57.982eV
Energy per atom: Epot =50.389eV Ekin = 7.600eV (T=632.180K) Etot = 57.989eV
Energy per atom: Epot =50.538eV Ekin = 7.456eV (T=620.199K) Etot = 57.993eV
Energy per atom: Epot =50.147eV Ekin = 7.838eV (T=652.030K) Etot = 57.985eV
Energy per atom: Epot =49.554eV Ekin = 8.423eV (T=700.716K) Etot = 57.977eV
Energy per atom: Epot =50.072eV Ekin = 7.911eV (T=658.077K) Etot = 57.983eV
Energy per atom: Epot =50.118eV Ekin = 7.865eV (T=654.227K) Etot = 57.983eV
Energy per atom: Epot =49.650eV Ekin = 8.328eV (T=692.759K) Etot = 57.978eV
Energy per atom: Epot =50.020eV Ekin = 7.959eV (T=662.045K) Etot = 57.978eV
Energy per atom: Epot =51.238eV Ekin = 6.751eV (T=561.614K) Etot = 57.990eV
Energy per atom: Epot =51.005eV Ekin = 6.988eV (T=581.277K) Etot = 57.992eV
Energy per atom: Epot =49.287eV Ekin = 8.700eV (T=723.724K) Etot = 57.987eV
Energy per atom: Epot =50.968eV Ekin = 7.029eV (T=584.725K) Etot = 57.997eV
Energy per atom: Epot =49.981eV Ekin = 8.009eV (T=666.256K) Etot = 57.990eV
Energy per atom: Epot =49.949eV Ekin = 8.042eV (T=668.965K) Etot = 57.990eV
Energy per atom: Epot =49.372eV Ekin = 8.612eV (T=716.367K) Etot = 57.984eV
Energy per atom: Epot =50.887eV Ekin = 7.106eV (T=591.083K) Etot = 57.993eV
Energy per atom: Epot =50.129eV Ekin = 7.860eV (T=653.817K) Etot = 57.988eV
Energy per atom: Epot =51.006eV Ekin = 6.982eV (T=580.789K) Etot = 57.988eV
Energy per atom: Epot =49.115eV Ekin = 8.864eV (T=737.398K) Etot = 57.980eV
Energy per atom: Epot =49.638eV Ekin = 8.347eV (T=694.360K) Etot = 57.985eV
Energy per atom: Epot =50.375eV Ekin = 7.614eV (T=633.410K) Etot = 57.989eV
Energy per atom: Epot =49.813eV Ekin = 8.176eV (T=680.141K) Etot = 57.989eV
Energy per atom: Epot =50.448eV Ekin = 7.539eV (T=627.166K) Etot = 57.988eV
Energy per atom: Epot =49.846eV Ekin = 8.136eV (T=676.765K) Etot = 57.982eV
Energy per atom: Epot =50.497eV Ekin = 7.487eV (T=622.796K) Etot = 57.984eV
Energy per atom: Epot =49.454eV Ekin = 8.524eV (T=709.059K) Etot = 57.978eV
Energy per atom: Epot =49.781eV Ekin = 8.199eV (T=682.052K) Etot = 57.980eV
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?